String with variable to check.

String with label for var, e.g. name of associated parameter.

(Named) character vector with extra variables in var which shouldn't be checked.

(Named) character vector with set of reference variables.

String with label for the reference

Data.frame with data.

String with type of message returned, either a 'warning' (default) or an error.

String with variable to check.

Logical, if TRUE the name of the summary statistic variable(s) (var) are included in the table. This is automatically set to TRUE if more than one variable(s) and is specified, and FALSE if only one variable is specified.

Extra parameters for the corresponding method.

summaryTable objects.

List of summaryTable objects.

(optional) String with name of a new variable tracking from which table each record originally come from.
The label for each table is extracted from the names of the summaryTables list, or 1:length(tables) if the list is not named.
If not specified (by default), the tables will be combined but the information on which input table: each record from the combined table belongs to will not be retained.

String indicating on which direction: 'row' or 'col' (a.k.a column) the information on the table appartenance (combineVar) will be displayed when the table is exported.

Combined summary table

Nested list with attributes of each summary table.

Data.frame with dataset to consider for the summary table.

nested list of parameters, specifying how the records of interest should be selected.
There are two ways to select a subset of interest:

• by specifying one unique variable of interest with:

  • var: string with column of data of interest

  • value: value of var of interest (only used if var is specified).
    If not specified only the values different than NA and ” are considered.

  • fctTest: string with name or directly comparison function to apply on var to select subset of interest versus value.
    The function should take var as first parameter and value to compare to as second parameter and returns a logical vector with TRUE or FALSE (of length var) if the condition is fullfilled.
    If not specified, the records with var equal to value are retained (fctTest is set to '==').

  • label specification:

    • label: string with label for the condition, includde in the new 'variable' column.
      If not specified and:

      • var is specified: label is extracted from labelVars if available or set to var otherwise.

      • var is not specified: label should be specified.

    • labelExtra: string with extra label, will be concatenated with label

• by specifying a combination of variable of interest with:

  • exprs: string with expression of columns of data to select subset of interest

  • label: string with complete label for the group

String with name of new variable to construct.

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

Default function to use to compare var and value specified in each sublist of paramsList.
This is only used if fctTest is not specified in each sublist.

Logical, if TRUE (FALSE by default) include also the entire data as an additional subgroup.

String of group label for the entire data in case includeAll is TRUE.

Data.frame with dataset to consider for the summary table.

Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts by row/column variable(s) are computed.
To also return counts of the rowVar in case other var are specified, you can include: 'all' in the var.
Missing values, if present, are filtered (also for the report of number of subjects/records).

Logical (FALSE by default) Should the total across all categories of var be included for the count table? Only used if var is a categorical variable.

(optional) Named list with functions for additional custom statistics to be computed.
Each function:

• has as parameter, either: 'x': the variable (var) to compute the summary statistic on or 'data': the entire dataset

• returns the corresponding summary statistic as a numeric vector

For example, to additionally compute the coefficient of variation, this can be set to: list(statCVPerc = function(x) sd(x)/mean(x)*100) (or cv).

String, variable of data with subject ID, 'USUBJID' by default.

Logical, if TRUE doesn't return any results if the variable is empty, otherwise return 0 for the counts and NA for summary statistics. Criterias to consider a variable empty are:

• for a continuous variable: all missing (NA)

• for a categorical variable: all missing or **category is included in the factor levels but not available in data**

By default, an empty variable are filtered.

String with type of table:

• 'summaryTable': summary table with statistics for numeric variable

• 'countTable': count table

• 'auto' (by default): 'summaryTable' if the variable is numeric, 'countTable' otherwise

String, 'error' (default), 'warning', or 'none'. Should an error, a warning, or nothing be produced if a continuous variable (var) contains different values for the same subject?

(optional) String with label for the data (NULL by default), included in the message/warning for checks.

(optional) Character vector with columns of data containing extra variables (besides var and subjectVar) that should be included in the message/warning for checks.

Data.frame with dataset to consider for the summary table.

Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts by row/column variable(s) are computed.
To also return counts of the rowVar in case other var are specified, you can include: 'all' in the var.
Missing values, if present, are filtered (also for the report of number of subjects/records).

Named character vector with label for each variable specified in var. By default, extracted from the labelVars. if not available, var is used.

Logical, should rows with no counts for the count var or varFlag variable(s) be included in the table? Either:

• logical of length 1, if TRUE (FALSE by default) rows with no count are included for all var

• a character vector containing categorical var for which zero counts rows should be included

Logical, if TRUE the name of the summary statistic variable(s) (var) are included in the table. This is automatically set to TRUE if more than one variable(s) and is specified, and FALSE if only one variable is specified.

Should the total across all categories of var be included for the count table? Only used for categorical variables (and var not 'all'). Either:

• logical of length 1, if TRUE (FALSE by default) include the total for all categorical var

• a character vector containing categorical var for which the total should be included

String with type of table:

• 'summaryTable': summary table with statistics for numeric variable

• 'countTable': count table

• 'auto' (by default): 'summaryTable' if the variable is numeric, 'countTable' otherwise

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Logical, if TRUE (FALSE by default), include rows with no records, based on all combinations of the rowVar (assuming nested variable(s)).

Data.frame with unique combinations of rowVar to be included in columns. Each column should correspond to colVar and as factor if the elements should be ordered in the final table.

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

Logical, if TRUE (FALSE by default), include columns with no records, based on all combinations of the columnVar (assuming nested variable(s)). If variable(s) are not nested, possible combinations can be specified via colVarDataLevels.

Data.frame with unique combinations of colVar to be included in columns. Each column should correspond to colVar and as factor if the elements should be ordered in the final table.

String, variable of data with subject ID, 'USUBJID' by default.

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

(optional) Named list with functions for additional custom statistics to be computed.
Each function:

• has as parameter, either: 'x': the variable (var) to compute the summary statistic on or 'data': the entire dataset

• returns the corresponding summary statistic as a numeric vector

For example, to additionally compute the coefficient of variation, this can be set to: list(statCVPerc = function(x) sd(x)/mean(x)*100) (or cv).

String, 'error' (default), 'warning', or 'none'. Should an error, a warning, or nothing be produced if a continuous variable (var) contains different values for the same subject (by row/column)?

Data.frame with dataset to consider for the summary table.

Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts by row/column variable(s) are computed.
To also return counts of the rowVar in case other var are specified, you can include: 'all' in the var.
Missing values, if present, are filtered (also for the report of number of subjects/records).

Character vector, subset of var with variable(s) of type 'flag' (with 'Y', 'N' or ” for empty/non specified value). Only the counts for records flagged (with 'Y') are retained.

Logical, should rows with no counts for the count var or varFlag variable(s) be included in the table? Either:

• logical of length 1, if TRUE (FALSE by default) rows with no count are included for all var

• a character vector containing categorical var for which zero counts rows should be included

Named character vector with label for each variable specified in var. By default, extracted from the labelVars. if not available, var is used.

Logical, if TRUE the name of the summary statistic variable(s) (var) are included in the table. This is automatically set to TRUE if more than one variable(s) and is specified, and FALSE if only one variable is specified.

String with general label for variable specified in var. In case of multiple variable in var, this will be included in the table header (see 'rowVarLab' attribute of the output).

String with general label for sub-group of categorical variable(s) for count table, 'Variable group' by default. This will be included in the final table header (see 'rowVarLab' attribute of the output).

Vector with elements to ignore in the var variable(s). The data records with such elements in var are filtered from the data at the start of the workflow.

This argument is deprecated, please use: 'varTotalInclude' instead.

Should the total across all categories of var be included for the count table? Only used for categorical variables (and var not 'all'). Either:

• logical of length 1, if TRUE (FALSE by default) include the total for all categorical var

• a character vector containing categorical var for which the total should be included

Logical, should the total per variable be included in a separated row (by default) or in the row containing the header of the variable?

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

Data.frame with unique combinations of colVar to be included in columns. Each column should correspond to colVar and as factor if the elements should be ordered in the final table.

String with column(s) considered to compute the total by, reported in the header of the table, by default same as colVar. Use: 'variable' to compute total by var (if multiple).

String with column(s) considered to compute the total by, used as denominator for the percentage computation, by default same as colVarTotal. Use: 'variable' to compute total by var (if multiple).

Logical, if TRUE (FALSE by default) include the summary statistics across columns in a separated column.

String, label for the total column 'Total' by default.

Logical, if TRUE (FALSE by default), include columns with no records, based on all combinations of the columnVar (assuming nested variable(s)). If variable(s) are not nested, possible combinations can be specified via colVarDataLevels.

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Data.frame with unique combinations of rowVar to be included in columns. Each column should correspond to colVar and as factor if the elements should be ordered in the final table.

Named character vector with label for the rowVar variable(s).

Specify how the rows should be ordered in the final table, either a:

• String among:

  • 'auto' (by default): if the variable is a factor, keep its order, otherwise order alphabetically

  • 'alphabetical': order alphabetically

  • 'total': order rows in decreasing order of the total number of subjects across all columns for this specific category.

• Function with input the summary table and output the ordered elements of the rowVar

To specify different ordering methods for different rowVar, specify a list of such elements, named with the rowVar variable. For the table output of computeSummaryStatisticsTable (long format), this order is also reflected in the levels of the row factor variable.

Function used to filter the data used to order the rows based on total counts (in case rowOrder is 'total'), To order rows based on one specific column category, e.g. to order based on the counts in the treatment column: function(x) subset(x, TRTP == "treatmentX")

String with category to be printed in the last row of each rowVar (if any, set to NULL if none).

Character vector with rowVar for which the total should be reported.
If the higher row variable is specified, the total across all rows is reported.
For the export, these variable(s) are formatted as factor with 'Total' as the first level.

Character vector with rowVarTotalInclude (not in rowVarInSepCol) for which the total should be included in a separated row labelled 'Total'. Otherwise (by default) the total is included in the header row of each category.

Character vector with a row variable used to categorize the row total.
Note that this is only used if row total(s) is/are requested via rowVarTotalInclude, and this variable should also be included in rowVar. This can be specified also for a specific row variable if the vector is named.
For example: c(ADECOD = "AESEV") to compute total by severity for row adverse event term in a typical adverse event count table (by System Organ Class and Adverse Event Term).

Character vector with row variables by which the total should be computed for the denominator for the percentage computation. By default the total is only computed only by column (NULL by default). If the total should be based on the total number of records per variable, rowVarTotalPerc should be set to 'variable'.

Logical, if TRUE (FALSE by default), include rows with no records, based on all combinations of the rowVar (assuming nested variable(s)).

String with type of table:

• 'summaryTable': summary table with statistics for numeric variable

• 'countTable': count table

• 'auto' (by default): 'summaryTable' if the variable is numeric, 'countTable' otherwise

String, variable of data with subject ID, 'USUBJID' by default.

Data.frame used to extract the Total number of subject per column in column header ('N = [X]'). It should contain the variables specified by colVarTotal. If not specified, the total number of subjects is extracted from the data.

Data.frame used to extract the total counts per column for the computation of the percentage.
By default, dataTotal is used.
It should contain the variables specified by colVarTotalPerc.

Data.frame used to extract the total count across all elements of the row variable, list of such data.frame for each rowVar variable.
If the dataset is specified by row variable, the list should be named with: variable X if the total across elements of variable X should be included. By default, data is used.

Data.frame from which the total across columns is extracted (in case colTotalInclude is TRUE) or list of such data.frame for each rowVar variable.
If the dataset is specified by row variable, the list should be named with: with:

• last row variable: for the dataset used in the total column for the most nested row variable

• higher row variable (X+1): for the dataset used for the total column and row total of X

• 'total': for the dataset used for the total column and general row total

If only a subset of the variables is specified in this list, data is used for the remaining variable(s) (or 'total') if needed.
This dataset (the one for 'total' if a list) is also used for:

• the header of the total column in case dataTotal is not specified

• the denominator of the percentages in the total column in case dataTotalPerc is not specified

By default, data is used.

(optional) Statistic(s) of interest to compute, either:

• string with the name of a default set of statistics available in the package, see section 'Formatted statistics' in in-text table statistics.
  See the corresponding type parameter of the getStatsData for more information on how the statistic is internally extracted.

• (expert mode) named list of language object (see is.language) of base summary statistics of interest, see section: 'Base statistics' in in-text table statistics.
  The names are reported in the header.
  If stats if of length 1, the name of the summary statistic is not included in the table.
  The statistics can be specified separately:

  • for each var (if multiple), by naming each element of the list: list(varName1 = list(...), varName2 = list())

  • and/or for each element in: statsVarBy, by naming each sublist.

String with variable in rowVar/colVar which the statistics should be computed by.
In this case, stats (nested list or not) should be additionally nested to specify the statistics for each element in statsVarBy.

(optional) Named list with functions for additional custom statistics to be computed.
Each function:

• has as parameter, either: 'x': the variable (var) to compute the summary statistic on or 'data': the entire dataset

• returns the corresponding summary statistic as a numeric vector

For example, to additionally compute the coefficient of variation, this can be set to: list(statCVPerc = function(x) sd(x)/mean(x)*100) (or cv).

String with general label for statistics, 'Statistic' by default. Only included if no statsVar if longer than 1.

String with 'base statistical variable' used to compute the percentage, either:

• 'statN' (by default): the number of subjects

• 'statm': the number of records

(optional) Function taking as input the summary table with computed statistics and returning a subset of the summary table.
Note: The filtering function should also handle records with :

• total for the column header: isTotal set to TRUE, and colVar/rowVar is NA.
  For example: filterFct = function(data) subset(data, isTotal & myColVar == "group 1")

• rowVar/colVar set to 'Total'/colTotalLab if rowVarTotalInclude/colTotalInclude is specified

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

Variable(s) of data for which separated table(s) should be created.

String with label for byVar, used to set the names of the output list of table(s).

String, 'error' (default), 'warning', or 'none'. Should an error, a warning, or nothing be produced if a continuous variable (var) contains different values for the same subject (by row/column)?

Data.frame with dataset to consider for the summary table.

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

Character vector with column(s) considered to compute the total. This could also contain 'variable'.

Character vector with row(s) considered to compute the total. This could also contain 'variable'.

Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts by row/column variable(s) are computed.
To also return counts of the rowVar in case other var are specified, you can include: 'all' in the var.
Missing values, if present, are filtered (also for the report of number of subjects/records).

String, label for the total column 'Total' by default.

Logical, if TRUE (FALSE by default) include the summary statistics across columns in a separated column.

Data.frame from which the total across columns is extracted (in case colTotalInclude is TRUE).

list with levels of each colVar

String, variable of data with subject ID, 'USUBJID' by default.

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

(optional) String with label for the data ('total' by default), included in the message/warning for checks.

A summaryTable object.

(flextable output) Logical, if TRUE (FALSE by default) the column header is merged.

(flextable output) Logical, if TRUE the file is in landscape format.
By default: FALSE if style is 'report' and TRUE if style is 'presentation'.

(flextable output) Margin in the document in inches (1 by default). This is used to specify the width of the table, from: [pageDim[1] - 2 * margin].

(flextable output) Base padding for row (in points), 14.4 by default (corresponds to 0.2 inches)

Character vector with title(s) for the table. Set to NULL (by default) if no title should be included. If multiple are specified, specified for each element of byVar (in order of the levels).

(flextable output) Character vector with footer(s) for the table. Set to NULL (by default) if no footer should be included.

(flextable output) String with table style, either 'report' or 'presentation'. This parameter affects the fontsize, font family, color of the text and background, and table dimensions of the table.

(flextable output) Named character vector with color for the table background/body/text/line, e.g. created with the getColorPaletteTable function.

(flextable output) String with font name, by default: 'Times' if style is 'report' and 'Tahoma' if style is 'presentation'.

(flextable output) Integer with font size, by default: 8 if style is 'report' and 10 if style is 'presentation'.

String with path of the file where the table should be exported. The file should have the extension: '.html'. If NULL, the summary table is not exported but only returned as output. If byVar is specified, each table is exported to a separated file with the suffix: 'file_[i].html' with i the index of the file.

Numeric vector of length 2 with page width and height.
Depending on outputType:

• 'flextable': in inches

• 'DT': in number of rows in the table.
  Currently only the height is used (e.g. c(NA, 4))

(expert mode) Column widths of the table. This is only used for flextable and DT tables.
For flextable, note that the widths should be set to fit into the document page (see getDimPage).

Character or factor variable with flag variable, should contain elements: 'Y' and 'N', or ” (for missing value).

Data.frame with dataset to consider for the summary table.

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts by row/column variable(s) are computed.
To also return counts of the rowVar in case other var are specified, you can include: 'all' in the var.
Missing values, if present, are filtered (also for the report of number of subjects/records).

Data.frame with dataset to consider for the summary table.

String with variable of data to sort.

Character vector with other variable(s) of data considered in the specific dimension.

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

String, label for the total column 'Total' by default.

Ordering method to use, either:

• String among:

  • 'auto': if var is a factor, keep its order, otherwise alphabetically

  • 'alphabetical': var is order in alphabetical order

  • 'total': var is ordered based on the totalVar variable, in decreasing order. The total count is extracted from the rows with all otherVars equal to 'Total'. If no otherVars is specified, consider all rows.

• Function to be applied on each subset to get the order elements of the variable

(optional) Function which returns a subset of the data of interest, to filter the total data considered for the ordering.

String with variable of data considered in case type is 'total', 'statN' by default.

String with last category (if any). Set to NULL if no specific category should be included as last element.

Vector.

Data.frame with data.

(optional) Data.frame with header. This should contain the same number of columns than data (+ if includeRownames is TRUE) and optionally multiple rows. Neighbouring cells with same content will be represented merged in the output.

Character vector with title(s) for the table. Set to NULL (by default) if no title should be included.

Logical, if TRUE (by default) rownames are included in the flextable object.

(flextable output) Logical, if TRUE (FALSE by default) the column header is merged.

Numeric vector.

Logical, should NA value(s) be removed (FALSE by default)?

Extra parameters for the corresponding method.

(DT output) Extra parameters passed to the getClinDT

A summaryTable object.

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Named character vector with label for the rowVar variable(s).

Character vector with rowVar that should be included in separated columns. By default (NULL), all row variables are nested in the first column of the table.
To include the groups within a var variable in a separated column, set: rowVarInSepCol == 'variableGroup'.

(flextable output) Named list with special formatting for the rowVar. Currently, only possibility is to set the variable elements in bold, with: list(var1 = "bold"). (Use 'variable' for var or 'variableGroup' for group within categorical variables.)

Character vector with rowVar for which the total should be reported.
If the higher row variable is specified, the total across all rows is reported.
For the export, these variable(s) are formatted as factor with 'Total' as the first level.

(flextable output) string with label for the row with total.

Character vector with rowVarTotalInclude (not in rowVarInSepCol) for which the total should be included in a separated row labelled 'Total'. Otherwise (by default) the total is included in the header row of each category.

(flextable output) Logical, if TRUE (by default) automatically merge rows, e.g. in case there is only one sub-category (e.g. categorical variable with only one group) or only one statistic per category.

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

String, label for the total column 'Total' by default.

Logical, if TRUE include the total of number of patients ('statN') in the column header.

(flextable output) Logical, if TRUE (FALSE by default) the column header is merged.

Character vector with columns of summaryTable with statistic variables. For the export: if not specified, all columns of data besides row, column variables, 'variable', 'variableGroup' and 'isTotal' are considered.

String with layout for the statistics names (in case more than one statistic is included), among:

• row (by default for 'flextable' output):
  All statistics are included in different rows in the first column of the table (after the row variable(s))

• 'col' (by default for 'DT' output):
  Statistics are included in separated columns (last row of the header).
  This option is not compatible with categorical variable(s).

• 'rowInSepCol':
  Statistics are included in different rows, but in a separated column than the rowVar variable(s)

String with label for the statistic value, 'StatisticValue' by default.
This is only included in the table if the statistics provided in stats are not named and if no colVar is specified.

Logical, if TRUE include the statistic label in the table.
By default only included if more than one statistic variables are available in the table.

String with placeholder used to fill the table for missing values, '-' by default. This value is typically used e.g. if not all statistics are computed for all specified row/col/var variables.

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

(Optional) Name of the file the table should be exported to, either:

• string (of length 1). In this case, depending on the file extension, the following is exported:

  • 'txt': summary table in long format ('data.frame-base' outputType)

  • 'docx': summary table in final format is exported ('flextable' outputType)

  • 'html': interactive summary table is exported ('DT' outputType)

• named character vector in case of multiple exports. The names should correspond to the options in outputType:

  • for 'data.frame-base' and 'data.frame': filename with 'txt' extension

  • for 'flextable': filename with 'docx' extension

  • for 'DT': filename with 'html' extension

If NULL (by default), the summary table is not exported but only returned as output. If byVar is specified, each table is exported to a separated file with the suffix: 'file_[i].[ext]' with i the index of the file (and [ext] the file extension).

Character vector with title(s) for the table. Set to NULL (by default) if no title should be included. If multiple are specified, specified for each element of byVar (in order of the levels).

String with output type:

• 'flextable' (by default): flextable object, with format for CSR, compatible with Word/PowerPoint export

• 'DT': datatable interactive table, compatible with html export

• 'data.frame': data.frame in wide format (with elements in colVar in different columns)

• 'data.frame-base': data.frame in long format (with elements in colVar in different rows), useful for QC

Numeric vector of length 2 with page width and height.
Depending on outputType:

• 'flextable': in inches

• 'DT': in number of rows in the table.
  Currently only the height is used (e.g. c(NA, 4))

(expert mode) Column widths of the table. This is only used for flextable and DT tables.
For flextable, note that the widths should be set to fit into the document page (see getDimPage).

(flextable output) Logical, if TRUE the file is in landscape format.
By default: FALSE if style is 'report' and TRUE if style is 'presentation'.

(flextable output) Margin in the document in inches (1 by default). This is used to specify the width of the table, from: [pageDim[1] - 2 * margin].

(flextable output) Base padding for row (in points), 14.4 by default (corresponds to 0.2 inches)

(flextable output) Character vector with footer(s) for the table. Set to NULL (by default) if no footer should be included.

(flextable output) String with table style, either 'report' or 'presentation'. This parameter affects the fontsize, font family, color of the text and background, and table dimensions of the table.

(flextable output) Named character vector with color for the table background/body/text/line, e.g. created with the getColorPaletteTable function.

(flextable output) Integer with font size, by default: 8 if style is 'report' and 10 if style is 'presentation'.

(flextable output) String with font name, by default: 'Times' if style is 'report' and 'Tahoma' if style is 'presentation'.

(flextable output) String mentioning how vertical lines should be included in the body of the table, either:

• 'none' (default): no vertical lines included

• 'auto': vertical lines included between sub-groups

(flextable output) String mentioning how horizontal lines should be included in the body of the table, either:

• 'none': no horizontal lines included

• 'auto' (default): horizontal lines included between sub-groups

(DT output) Character vector with variables of the summary table which should be expanded in the data.

(DT output) Character vector with variables of summaryTable which shouldn't be escaped in the table (e.g. containing URLs).

(DT output) Character vector with variables of summaryTable that should be represented as a bar.

flextable object, or list of such objects

String with path of the file where the table should be exported. The file should have the extension: '.html'. If NULL, the summary table is not exported but only returned as output. If byVar is specified, each table is exported to a separated file with the suffix: 'file_[i].html' with i the index of the file.

(flextable output) Logical, if TRUE the file is in landscape format.
By default: FALSE if style is 'report' and TRUE if style is 'presentation'.

In case object is list: integer vector with indices of list item after which a page break should be included in the final document.

Summary table as provided by the formatSummaryStatisticsTable.

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Named character vector with label for the rowVar variable(s).

Character vector with rowVar that should be included in separated columns. By default (NULL), all row variables are nested in the first column of the table.
To include the groups within a var variable in a separated column, set: rowVarInSepCol == 'variableGroup'.

Character vector with columns of summaryTable with statistic variables. For the export: if not specified, all columns of data besides row, column variables, 'variable', 'variableGroup' and 'isTotal' are considered.

String with layout for the statistics names (in case more than one statistic is included), among:

• row (by default for 'flextable' output):
  All statistics are included in different rows in the first column of the table (after the row variable(s))

• 'col' (by default for 'DT' output):
  Statistics are included in separated columns (last row of the header).
  This option is not compatible with categorical variable(s).

• 'rowInSepCol':
  Statistics are included in different rows, but in a separated column than the rowVar variable(s)

String with label for the statistic value, 'StatisticValue' by default.
This is only included in the table if the statistics provided in stats are not named and if no colVar is specified.

Character vector with title(s) for the table. Set to NULL (by default) if no title should be included. If multiple are specified, specified for each element of byVar (in order of the levels).

(DT output) Character vector with variables of the summary table which should be expanded in the data.

(DT output) Character vector with variables of summaryTable which shouldn't be escaped in the table (e.g. containing URLs).

(DT output) Character vector with variables of summaryTable that should be represented as a bar.

Numeric vector of length 2 with page width and height.
Depending on outputType:

• 'flextable': in inches

• 'DT': in number of rows in the table.
  Currently only the height is used (e.g. c(NA, 4))

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

String with path of the file where the table should be exported. The file should have the extension: '.docx'. If NULL, the summary table is not exported but only returned as output. If byVar is specified, each table is exported to a separated file with the suffix: 'file_[i].docx' with i the index of the file.

(DT output) Extra parameters passed to the getClinDT

Summary table as provided by the formatSummaryStatisticsTable

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Character vector with rowVar that should be included in separated columns. By default (NULL), all row variables are nested in the first column of the table.
To include the groups within a var variable in a separated column, set: rowVarInSepCol == 'variableGroup'.

Character vector with rowVar for which the total should be reported.
If the higher row variable is specified, the total across all rows is reported.
For the export, these variable(s) are formatted as factor with 'Total' as the first level.

String with layout for the statistics names (in case more than one statistic is included), among:

• row (by default for 'flextable' output):
  All statistics are included in different rows in the first column of the table (after the row variable(s))

• 'col' (by default for 'DT' output):
  Statistics are included in separated columns (last row of the header).
  This option is not compatible with categorical variable(s).

• 'rowInSepCol':
  Statistics are included in different rows, but in a separated column than the rowVar variable(s)

Character vector with columns of summaryTable with statistic variables. For the export: if not specified, all columns of data besides row, column variables, 'variable', 'variableGroup' and 'isTotal' are considered.

Logical, if TRUE include the statistic label in the table.
By default only included if more than one statistic variables are available in the table.

Named character vector with label for the rowVar variable(s).

Character vector with rowVarTotalInclude (not in rowVarInSepCol) for which the total should be included in a separated row labelled 'Total'. Otherwise (by default) the total is included in the header row of each category.

(flextable output) String mentioning how vertical lines should be included in the body of the table, either:

• 'none' (default): no vertical lines included

• 'auto': vertical lines included between sub-groups

(flextable output) String mentioning how horizontal lines should be included in the body of the table, either:

• 'none': no horizontal lines included

• 'auto' (default): horizontal lines included between sub-groups

(flextable output) Logical, if TRUE (by default) automatically merge rows, e.g. in case there is only one sub-category (e.g. categorical variable with only one group) or only one statistic per category.

(flextable output) Named list with special formatting for the rowVar. Currently, only possibility is to set the variable elements in bold, with: list(var1 = "bold"). (Use 'variable' for var or 'variableGroup' for group within categorical variables.)

(flextable output) string with label for the row with total.

(flextable output) Logical, if TRUE (FALSE by default) the column header is merged.

(flextable output) Logical, if TRUE the file is in landscape format.
By default: FALSE if style is 'report' and TRUE if style is 'presentation'.

(flextable output) Margin in the document in inches (1 by default). This is used to specify the width of the table, from: [pageDim[1] - 2 * margin].

(flextable output) Base padding for row (in points), 14.4 by default (corresponds to 0.2 inches)

Character vector with title(s) for the table. Set to NULL (by default) if no title should be included. If multiple are specified, specified for each element of byVar (in order of the levels).

(flextable output) Character vector with footer(s) for the table. Set to NULL (by default) if no footer should be included.

(flextable output) String with table style, either 'report' or 'presentation'. This parameter affects the fontsize, font family, color of the text and background, and table dimensions of the table.

(flextable output) Named character vector with color for the table background/body/text/line, e.g. created with the getColorPaletteTable function.

(flextable output) String with font name, by default: 'Times' if style is 'report' and 'Tahoma' if style is 'presentation'.

(flextable output) Integer with font size, by default: 8 if style is 'report' and 10 if style is 'presentation'.

String with path of the file where the table should be exported. The file should have the extension: '.html'. If NULL, the summary table is not exported but only returned as output. If byVar is specified, each table is exported to a separated file with the suffix: 'file_[i].html' with i the index of the file.

Numeric vector of length 2 with page width and height.
Depending on outputType:

• 'flextable': in inches

• 'DT': in number of rows in the table.
  Currently only the height is used (e.g. c(NA, 4))

(expert mode) Column widths of the table. This is only used for flextable and DT tables.
For flextable, note that the widths should be set to fit into the document page (see getDimPage).

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

data.frame with data used in table, summary table for body or header data.frame for the header.

Corresponding flextable.

String with font name, 'Times' by default.

string with part of the table to consider, see compose.

Integer with font size, 8 by default.

Integer with base row index (if different than 0).

Logical (FALSE by default) should the superscript/subscript be indicated in bold?

Numeric vector with percentage(s)

Integer of length 1, number of decimals used to round the percentage, 1 by default.

A summaryTable object.

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

String, label for the total column 'Total' by default.

Logical, if TRUE include the total of number of patients ('statN') in the column header.

Character vector with columns of summaryTable with statistic variables. For the export: if not specified, all columns of data besides row, column variables, 'variable', 'variableGroup' and 'isTotal' are considered.

Logical, if TRUE include the statistic label in the table.
By default only included if more than one statistic variables are available in the table.

String with layout for the statistics names (in case more than one statistic is included), among:

• row (by default for 'flextable' output):
  All statistics are included in different rows in the first column of the table (after the row variable(s))

• 'col' (by default for 'DT' output):
  Statistics are included in separated columns (last row of the header).
  This option is not compatible with categorical variable(s).

• 'rowInSepCol':
  Statistics are included in different rows, but in a separated column than the rowVar variable(s)

String with label for the statistic value, 'StatisticValue' by default.
This is only included in the table if the statistics provided in stats are not named and if no colVar is specified.

String with placeholder used to fill the table for missing values, '-' by default. This value is typically used e.g. if not all statistics are computed for all specified row/col/var variables.

A summaryTable object.

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Character vector with rowVar that should be included in separated columns. By default (NULL), all row variables are nested in the first column of the table.
To include the groups within a var variable in a separated column, set: rowVarInSepCol == 'variableGroup'.

Character vector with rowVar for which the total should be reported.
If the higher row variable is specified, the total across all rows is reported.
For the export, these variable(s) are formatted as factor with 'Total' as the first level.

String with layout for the statistics names (in case more than one statistic is included), among:

• row (by default for 'flextable' output):
  All statistics are included in different rows in the first column of the table (after the row variable(s))

• 'col' (by default for 'DT' output):
  Statistics are included in separated columns (last row of the header).
  This option is not compatible with categorical variable(s).

• 'rowInSepCol':
  Statistics are included in different rows, but in a separated column than the rowVar variable(s)

Character vector with columns of summaryTable with statistic variables. For the export: if not specified, all columns of data besides row, column variables, 'variable', 'variableGroup' and 'isTotal' are considered.

Logical, if TRUE include the statistic label in the table.
By default only included if more than one statistic variables are available in the table.

Named character vector with label for the rowVar variable(s).

Character vector with rowVarTotalInclude (not in rowVarInSepCol) for which the total should be included in a separated row labelled 'Total'. Otherwise (by default) the total is included in the header row of each category.

(flextable output) String mentioning how vertical lines should be included in the body of the table, either:

• 'none' (default): no vertical lines included

• 'auto': vertical lines included between sub-groups

(flextable output) String mentioning how horizontal lines should be included in the body of the table, either:

• 'none': no horizontal lines included

• 'auto' (default): horizontal lines included between sub-groups

(flextable output) Logical, if TRUE (by default) automatically merge rows, e.g. in case there is only one sub-category (e.g. categorical variable with only one group) or only one statistic per category.

(flextable output) Named list with special formatting for the rowVar. Currently, only possibility is to set the variable elements in bold, with: list(var1 = "bold"). (Use 'variable' for var or 'variableGroup' for group within categorical variables.)

(flextable output) string with label for the row with total.

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

Numeric vector.

Logical, should NA value(s) be removed (FALSE by default)?

Numeric vector.

Logical, should NA value(s) be removed (FALSE by default)?

Numeric vector.

Logical, should NA value(s) be removed (FALSE by default)?

Numeric vector.

Logical, should NA value(s) be removed (FALSE by default)?

String with attribute name.

Object with default value for attribute, NULL by default.

String with style of report. Either 'report' or 'presentation'. By default, the style is 'report'.

Character vector with dimension of interest, among: 'width', 'height', multiple are possible. By default: c("width", "height")

Logical, if TRUE the table is presented in landscape format.
By default: TRUE for style: 'report', FALSE for style: 'presentation'.

Margin in the document in inches, 1 by default.

(optional) Numeric vector of length 2 with page width and height in inches in portrait format, in case page dimensions differ from the default implemented report/presentation. These dimensions should include the margins.

String with table style, either 'report' (by default, a4 format) or 'presentation'

data.frame with data used in table.

Corresponding flextable.

Logical, if TRUE add a border.

Integer vector with index(ices) of column(s) to highlight (only applies for style: 'presentation'). 0 for rownames (if present). Colors for:

• highlighted columns is specified in colorTable["headerBackgroundHighlight"]

• non highlighted columns is specified in colorTable["headerBackground"]

String with the column of the data used for alternating the body background colors of the table.

String with font name, 'Times' by default.

Integer with font size, 8 by default.

Logical, if TRUE the table is presented in landscape format.
By default: TRUE for style: 'report', FALSE for style: 'presentation'.

String with table style, either 'report' (by default, a4 format) or 'presentation'

Margin in the document in inches, 1 by default.

Logical, if TRUE adjust column widths, to comply to specification of landscape, margin and pageDim (only set to FALSE if e.g. table dimensions are pre-set with the specified ft).

Named character vector with color for the table, see output of getColorPaletteTable for required elements.

Logical, if TRUE (by default), default alignment is set ('center' in all table).

Character vector with title(s) for the table. Set to NULL (by default) if no title should be included. Only available if ft is not specified.

(optional) Numeric vector of length 2 with page width and height in inches in portrait format, in case page dimensions differ from the default implemented report/presentation. These dimensions should include the margins.

Logical, if TRUE (by default) rownames are included in the flextable object.

Numeric vector.

Any parameters for the getNDecimals function.

Numeric vector.

Numeric vector.

Logical (TRUE by default), should the rule be applied?

Character vector with rule to use to derive the number of parameters. Currently only: '1' is implemented.

• '1': standard rule for the number of decimals for individual values for a continuous variable:

  • value < 1 ('very small values'): 3

  • value < 10: 2

  • value in [10, 1000[: 1

  • value >= 1000: 0

Logical (TRUE by default), should the number of decimals be extracted based on the input data x?

Numeric vector.

Numeric vector.

Character vector with rule to use to derive the number of parameters. Currently only: '1' is implemented.

• '1': standard rule for the number of decimals for individual values for a continuous variable:

  • value < 1 ('very small values'): 3

  • value < 10: 2

  • value in [10, 1000[: 1

  • value >= 1000: 0

String.

String with start pattern.

String with end pattern.

String with type of formatting

Summary table.

Character vector with initial statistics names.

Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts by row/column variable(s) are computed.
To also return counts of the rowVar in case other var are specified, you can include: 'all' in the var.
Missing values, if present, are filtered (also for the report of number of subjects/records).

(Optionally) named list of expression or call object of summary statistics of interest. The names are reported in the header. The following variables are recognized, if the table is a:

• 'summaryTable':

  • 'statN': number of subjects

  • 'statMean': mean of var

  • 'statSD': standard deviation of var

  • 'statSE': standard error of var

  • 'statMedian': median of var

  • 'statMin': minimum of var

  • 'statMax': maximum of var

  • 'statPerc': percentage of subjects

  • 'statm': number of records

• 'countTable':

  • 'statN': number of subjects

  • 'statPercN': percentage of subjects

  • 'statm': number of records

If stats if of length 1, the name of the summary statistic is not included in the table. The statistics can be specified for each var (if multiple), by naming each element of the list: list(varName1 = list(...), varName2 = list()) and/or for each element in: statsVarBy, by naming each sublist.

Character vector with colnames of data by which the statistics should be computed. In this case, stats (nested list or not) should be additionally nested to specify the statistics for each element in statsVarBy.

Character vector with type of statistics (multiple are possible). Available statistics are specified in the section 'Formatted statistics' and formatting in 'Statistics formatting' in in-text table statistics.

Logical, should the statistics name be included (TRUE by default)? This is applied for the statistic names used in each for the set defined in type; and for the label of the list if type is of length 2. If there are multiple type or statistics within a set, the names are retained (to avoid confusion).

(optional, recommended for continuous variable) Numeric vector for which the statistics should be computed on.
This is used to derive the number of decimals to include for a continuous variable.
If not specified, the values are rounded with formatC.

Integer with base number of decimals for continuous variable, or function returning this number based on x (getNDecimals by default).

Integer with number of decimals for number of subjects/records (0 by default).

Function used to format the percentages (see formatPercentage for default behaviour).

Data.frame with dataset to consider for the summary table.

(optional, recommended for continuous variable) Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts of the entire dataset are computed.
It is passed to the x parameter of getStats.

Character vector with type of statistics to extract, among:

• 'default': default sets of statistics, see types: 'summary-default' and 'count-default' in getStats

• 'all': all computed statistics, see types: 'summary' and 'count' in getStats

• any formatted statistics as implemented in getStats, see section 'Formatted statistics' in in-text table statistics.

To specify statistics for a continuous (numeric) or categorical variable separately, this vector can be named with: 'cont' or 'cat' respectively (elements not named are used for both continuous and categorical variables).

List with extra statistics to include, or function to apply on each var (e.g. depending on the class of var) to get such statistic.

(optional) Named list with extra arguments for getStats for continuous (name: 'cont') or categorical variable (name: 'cat') specifically.

Extra parameters passed to the getStats function (independent of the variable type).

Data.frame with dataset to consider for the summary table.

Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts by row/column variable(s) are computed.
To also return counts of the rowVar in case other var are specified, you can include: 'all' in the var.
Missing values, if present, are filtered (also for the report of number of subjects/records).

Character vector, subset of var with variable(s) of type 'flag' (with 'Y', 'N' or ” for empty/non specified value). Only the counts for records flagged (with 'Y') are retained.

Named character vector with label for each variable specified in var. By default, extracted from the labelVars. if not available, var is used.

Logical, if TRUE the name of the summary statistic variable(s) (var) are included in the table. This is automatically set to TRUE if more than one variable(s) and is specified, and FALSE if only one variable is specified.

Logical, should rows with no counts for the count var or varFlag variable(s) be included in the table? Either:

• logical of length 1, if TRUE (FALSE by default) rows with no count are included for all var

• a character vector containing categorical var for which zero counts rows should be included

Vector with elements to ignore in the var variable(s). The data records with such elements in var are filtered from the data at the start of the workflow.

String with general label for variable specified in var. In case of multiple variable in var, this will be included in the table header (see 'rowVarLab' attribute of the output).

String with general label for sub-group of categorical variable(s) for count table, 'Variable group' by default. This will be included in the final table header (see 'rowVarLab' attribute of the output).

This argument is deprecated, please use: 'varTotalInclude' instead.

Should the total across all categories of var be included for the count table? Only used for categorical variables (and var not 'all'). Either:

• logical of length 1, if TRUE (FALSE by default) include the total for all categorical var

• a character vector containing categorical var for which the total should be included

Logical, should the total per variable be included in a separated row (by default) or in the row containing the header of the variable?

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Named character vector with label for the rowVar variable(s).

Data.frame with unique combinations of rowVar to be included in columns. Each column should correspond to colVar and as factor if the elements should be ordered in the final table.

Specify how the rows should be ordered in the final table, either a:

• String among:

  • 'auto' (by default): if the variable is a factor, keep its order, otherwise order alphabetically

  • 'alphabetical': order alphabetically

  • 'total': order rows in decreasing order of the total number of subjects across all columns for this specific category.

• Function with input the summary table and output the ordered elements of the rowVar

To specify different ordering methods for different rowVar, specify a list of such elements, named with the rowVar variable. For the table output of computeSummaryStatisticsTable (long format), this order is also reflected in the levels of the row factor variable.

Function used to filter the data used to order the rows based on total counts (in case rowOrder is 'total'), To order rows based on one specific column category, e.g. to order based on the counts in the treatment column: function(x) subset(x, TRTP == "treatmentX")

String with category to be printed in the last row of each rowVar (if any, set to NULL if none).

Character vector with rowVar that should be included in separated columns. By default (NULL), all row variables are nested in the first column of the table.
To include the groups within a var variable in a separated column, set: rowVarInSepCol == 'variableGroup'.

(flextable output) Named list with special formatting for the rowVar. Currently, only possibility is to set the variable elements in bold, with: list(var1 = "bold"). (Use 'variable' for var or 'variableGroup' for group within categorical variables.)

Character vector with rowVar for which the total should be reported.
If the higher row variable is specified, the total across all rows is reported.
For the export, these variable(s) are formatted as factor with 'Total' as the first level.

Character vector with a row variable used to categorize the row total.
Note that this is only used if row total(s) is/are requested via rowVarTotalInclude, and this variable should also be included in rowVar. This can be specified also for a specific row variable if the vector is named.
For example: c(ADECOD = "AESEV") to compute total by severity for row adverse event term in a typical adverse event count table (by System Organ Class and Adverse Event Term).

Character vector with rowVarTotalInclude (not in rowVarInSepCol) for which the total should be included in a separated row labelled 'Total'. Otherwise (by default) the total is included in the header row of each category.

(flextable output) string with label for the row with total.

Logical, if TRUE (FALSE by default), include rows with no records, based on all combinations of the rowVar (assuming nested variable(s)).

(flextable output) Logical, if TRUE (by default) automatically merge rows, e.g. in case there is only one sub-category (e.g. categorical variable with only one group) or only one statistic per category.

String with placeholder used to fill the table for missing values, '-' by default. This value is typically used e.g. if not all statistics are computed for all specified row/col/var variables.

Character vector with row variables by which the total should be computed for the denominator for the percentage computation. By default the total is only computed only by column (NULL by default). If the total should be based on the total number of records per variable, rowVarTotalPerc should be set to 'variable'.

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

String with column(s) considered to compute the total by, reported in the header of the table, by default same as colVar. Use: 'variable' to compute total by var (if multiple).

String with column(s) considered to compute the total by, used as denominator for the percentage computation, by default same as colVarTotal. Use: 'variable' to compute total by var (if multiple).

Logical, if TRUE (FALSE by default), include columns with no records, based on all combinations of the columnVar (assuming nested variable(s)). If variable(s) are not nested, possible combinations can be specified via colVarDataLevels.

Data.frame with unique combinations of colVar to be included in columns. Each column should correspond to colVar and as factor if the elements should be ordered in the final table.

Logical, if TRUE (FALSE by default) include the summary statistics across columns in a separated column.

String, label for the total column 'Total' by default.

(optional) Statistic(s) of interest to compute, either:

• string with the name of a default set of statistics available in the package, see section 'Formatted statistics' in in-text table statistics.
  See the corresponding type parameter of the getStatsData for more information on how the statistic is internally extracted.

• (expert mode) named list of language object (see is.language) of base summary statistics of interest, see section: 'Base statistics' in in-text table statistics.
  The names are reported in the header.
  If stats if of length 1, the name of the summary statistic is not included in the table.
  The statistics can be specified separately:

  • for each var (if multiple), by naming each element of the list: list(varName1 = list(...), varName2 = list())

  • and/or for each element in: statsVarBy, by naming each sublist.

(optional) Named list with functions for additional custom statistics to be computed.
Each function:

• has as parameter, either: 'x': the variable (var) to compute the summary statistic on or 'data': the entire dataset

• returns the corresponding summary statistic as a numeric vector

For example, to additionally compute the coefficient of variation, this can be set to: list(statCVPerc = function(x) sd(x)/mean(x)*100) (or cv).

String with variable in rowVar/colVar which the statistics should be computed by.
In this case, stats (nested list or not) should be additionally nested to specify the statistics for each element in statsVarBy.

String with 'base statistical variable' used to compute the percentage, either:

• 'statN' (by default): the number of subjects

• 'statm': the number of records

String with general label for statistics, 'Statistic' by default. Only included if no statsVar if longer than 1.

String with label for the statistic value, 'StatisticValue' by default.
This is only included in the table if the statistics provided in stats are not named and if no colVar is specified.

Logical, if TRUE include the statistic label in the table.
By default only included if more than one statistic variables are available in the table.

String, variable of data with subject ID, 'USUBJID' by default.

(optional) Function taking as input the summary table with computed statistics and returning a subset of the summary table.
Note: The filtering function should also handle records with :

• total for the column header: isTotal set to TRUE, and colVar/rowVar is NA.
  For example: filterFct = function(data) subset(data, isTotal & myColVar == "group 1")

• rowVar/colVar set to 'Total'/colTotalLab if rowVarTotalInclude/colTotalInclude is specified

Data.frame used to extract the Total number of subject per column in column header ('N = [X]'). It should contain the variables specified by colVarTotal. If not specified, the total number of subjects is extracted from the data.

Data.frame used to extract the total counts per column for the computation of the percentage.
By default, dataTotal is used.
It should contain the variables specified by colVarTotalPerc.

Data.frame used to extract the total count across all elements of the row variable, list of such data.frame for each rowVar variable.
If the dataset is specified by row variable, the list should be named with: variable X if the total across elements of variable X should be included. By default, data is used.

Data.frame from which the total across columns is extracted (in case colTotalInclude is TRUE) or list of such data.frame for each rowVar variable.
If the dataset is specified by row variable, the list should be named with: with:

• last row variable: for the dataset used in the total column for the most nested row variable

• higher row variable (X+1): for the dataset used for the total column and row total of X

• 'total': for the dataset used for the total column and general row total

If only a subset of the variables is specified in this list, data is used for the remaining variable(s) (or 'total') if needed.
This dataset (the one for 'total' if a list) is also used for:

• the header of the total column in case dataTotal is not specified

• the denominator of the percentages in the total column in case dataTotalPerc is not specified

By default, data is used.

String with type of table:

• 'summaryTable': summary table with statistics for numeric variable

• 'countTable': count table

• 'auto' (by default): 'summaryTable' if the variable is numeric, 'countTable' otherwise

Variable(s) of data for which separated table(s) should be created.

String with label for byVar, used to set the names of the output list of table(s).

String, 'error' (default), 'warning', or 'none'. Should an error, a warning, or nothing be produced if a continuous variable (var) contains different values for the same subject (by row/column)?

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

String with output type:

• 'flextable' (by default): flextable object, with format for CSR, compatible with Word/PowerPoint export

• 'DT': datatable interactive table, compatible with html export

• 'data.frame': data.frame in wide format (with elements in colVar in different columns)

• 'data.frame-base': data.frame in long format (with elements in colVar in different rows), useful for QC

String with layout for the statistics names (in case more than one statistic is included), among:

• row (by default for 'flextable' output):
  All statistics are included in different rows in the first column of the table (after the row variable(s))

• 'col' (by default for 'DT' output):
  Statistics are included in separated columns (last row of the header).
  This option is not compatible with categorical variable(s).

• 'rowInSepCol':
  Statistics are included in different rows, but in a separated column than the rowVar variable(s)

(flextable output) Logical, if TRUE the file is in landscape format.
By default: FALSE if style is 'report' and TRUE if style is 'presentation'.

(flextable output) Margin in the document in inches (1 by default). This is used to specify the width of the table, from: [pageDim[1] - 2 * margin].

(flextable output) Base padding for row (in points), 14.4 by default (corresponds to 0.2 inches)

Character vector with title(s) for the table. Set to NULL (by default) if no title should be included. If multiple are specified, specified for each element of byVar (in order of the levels).

(flextable output) Character vector with footer(s) for the table. Set to NULL (by default) if no footer should be included.

(Optional) Name of the file the table should be exported to, either:

• string (of length 1). In this case, depending on the file extension, the following is exported:

  • 'txt': summary table in long format ('data.frame-base' outputType)

  • 'docx': summary table in final format is exported ('flextable' outputType)

  • 'html': interactive summary table is exported ('DT' outputType)

• named character vector in case of multiple exports. The names should correspond to the options in outputType:

  • for 'data.frame-base' and 'data.frame': filename with 'txt' extension

  • for 'flextable': filename with 'docx' extension

  • for 'DT': filename with 'html' extension

If NULL (by default), the summary table is not exported but only returned as output. If byVar is specified, each table is exported to a separated file with the suffix: 'file_[i].[ext]' with i the index of the file (and [ext] the file extension).

(flextable output) String with table style, either 'report' or 'presentation'. This parameter affects the fontsize, font family, color of the text and background, and table dimensions of the table.

(flextable output) Named character vector with color for the table background/body/text/line, e.g. created with the getColorPaletteTable function.

Logical, if TRUE include the total of number of patients ('statN') in the column header.

(flextable output) Logical, if TRUE (FALSE by default) the column header is merged.

(flextable output) Integer with font size, by default: 8 if style is 'report' and 10 if style is 'presentation'.

(flextable output) String with font name, by default: 'Times' if style is 'report' and 'Tahoma' if style is 'presentation'.

(flextable output) String mentioning how vertical lines should be included in the body of the table, either:

• 'none' (default): no vertical lines included

• 'auto': vertical lines included between sub-groups

(flextable output) String mentioning how horizontal lines should be included in the body of the table, either:

• 'none': no horizontal lines included

• 'auto' (default): horizontal lines included between sub-groups

Numeric vector of length 2 with page width and height.
Depending on outputType:

• 'flextable': in inches

• 'DT': in number of rows in the table.
  Currently only the height is used (e.g. c(NA, 4))

(expert mode) Column widths of the table. This is only used for flextable and DT tables.
For flextable, note that the widths should be set to fit into the document page (see getDimPage).

(DT output) Character vector with variables of the summary table which should be expanded in the data.

(DT output) Character vector with variables of summaryTable which shouldn't be escaped in the table (e.g. containing URLs).

(DT output) Character vector with variables of summaryTable that should be represented as a bar.

(DT output) Extra parameters passed to the getClinDT

(DT output) Character vector with variables of the summary table which should be expanded in the data.

(DT output) Numeric vector of length 2 with page width and height, in number of rows (currently only the height is used (e.g. c(NA, 4))

(DT output) Character vector with variables of summaryTable which shouldn't be escaped in the table (e.g. containing URLs).

(DT output) Character vector with variables of summaryTable that should be represented as a bar.

String with path of the file where the table should be exported. The file should have the extension: '.docx'. If NULL, the summary table is not exported but only returned as output. If byVar is specified, each table is exported to a separated file with the suffix: 'file_[i].docx' with i the index of the file.

Data.frame with dataset to consider for the summary table.

A summaryTable object.

Character vector with variable(s) of data, to compute statistics on.
If NULL (by default), counts by row/column variable(s) are computed.
To also return counts of the rowVar in case other var are specified, you can include: 'all' in the var.
Missing values, if present, are filtered (also for the report of number of subjects/records).

Character vector, subset of var with variable(s) of type 'flag' (with 'Y', 'N' or ” for empty/non specified value). Only the counts for records flagged (with 'Y') are retained.

Logical, if TRUE the name of the summary statistic variable(s) (var) are included in the table. This is automatically set to TRUE if more than one variable(s) and is specified, and FALSE if only one variable is specified.

Character vector with variable(s) to be included in the rows. If multiple variables are specified, the variables should be sorted in hierarchical order (e.g. body system class before adverse event term) and are nested in the table.

Character vector with rowVar that should be included in separated columns. By default (NULL), all row variables are nested in the first column of the table.
To include the groups within a var variable in a separated column, set: rowVarInSepCol == 'variableGroup'.

Named character vector with label for the rowVar variable(s).

Character vector with columns of summaryTable with statistic variables. For the export: if not specified, all columns of data besides row, column variables, 'variable', 'variableGroup' and 'isTotal' are considered.

Character vector with rowVar for which the total should be reported.
If the higher row variable is specified, the total across all rows is reported.
For the export, these variable(s) are formatted as factor with 'Total' as the first level.

Character vector with rowVarTotalInclude (not in rowVarInSepCol) for which the total should be included in a separated row labelled 'Total'. Otherwise (by default) the total is included in the header row of each category.

Character vector with variable(s) to be included in columns. If multiple variables are specified, the variables should be sorted in hierarchical order, and are included in multi-columns layout.
Use: 'variable' to include the variables to summarize: var (if multiple) in different columns.

Logical, if TRUE (FALSE by default) include the summary statistics across columns in a separated column.

String, label for the total column 'Total' by default.

String, variable of data with subject ID, 'USUBJID' by default.

String with layout for the statistics names (in case more than one statistic is included), among:

• row (by default for 'flextable' output):
  All statistics are included in different rows in the first column of the table (after the row variable(s))

• 'col' (by default for 'DT' output):
  Statistics are included in separated columns (last row of the header).
  This option is not compatible with categorical variable(s).

• 'rowInSepCol':
  Statistics are included in different rows, but in a separated column than the rowVar variable(s)

String with label for the statistic value, 'StatisticValue' by default.
This is only included in the table if the statistics provided in stats are not named and if no colVar is specified.

(optional) Named list with functions for additional custom statistics to be computed.
Each function:

• has as parameter, either: 'x': the variable (var) to compute the summary statistic on or 'data': the entire dataset

• returns the corresponding summary statistic as a numeric vector

For example, to additionally compute the coefficient of variation, this can be set to: list(statCVPerc = function(x) sd(x)/mean(x)*100) (or cv).

String with type of table:

• 'summaryTable': summary table with statistics for numeric variable

• 'countTable': count table

• 'auto' (by default): 'summaryTable' if the variable is numeric, 'countTable' otherwise

Logical, if TRUE include the statistic label in the table.
By default only included if more than one statistic variables are available in the table.

Character vector with title(s) for the table. Set to NULL (by default) if no title should be included. If multiple are specified, specified for each element of byVar (in order of the levels).

Numeric vector of length 2 with page width and height.
Depending on outputType:

• 'flextable': in inches

• 'DT': in number of rows in the table.
  Currently only the height is used (e.g. c(NA, 4))

(expert mode) Column widths of the table. This is only used for flextable and DT tables.
For flextable, note that the widths should be set to fit into the document page (see getDimPage).

(optional) Named character vector with label for the row, column variable(s) or variable(s) to summarize.
Labels specified via dedicated parameter: e.g. rowVarLab, colVarLab, varLab have priority on this parameter.

(flextable output) String with table style, either 'report' or 'presentation'. This parameter affects the fontsize, font family, color of the text and background, and table dimensions of the table.

(flextable output) string with label for the row with total.

(flextable output) Logical, if TRUE (by default) automatically merge rows, e.g. in case there is only one sub-category (e.g. categorical variable with only one group) or only one statistic per category.

(flextable output) Named list with special formatting for the rowVar. Currently, only possibility is to set the variable elements in bold, with: list(var1 = "bold"). (Use 'variable' for var or 'variableGroup' for group within categorical variables.)

(flextable output) Base padding for row (in points), 14.4 by default (corresponds to 0.2 inches)

(flextable output) String with font name, by default: 'Times' if style is 'report' and 'Tahoma' if style is 'presentation'.

(flextable output) Integer with font size, by default: 8 if style is 'report' and 10 if style is 'presentation'.

(flextable output) Margin in the document in inches (1 by default). This is used to specify the width of the table, from: [pageDim[1] - 2 * margin].

(flextable output) Named character vector with color for the table background/body/text/line, e.g. created with the getColorPaletteTable function.

(flextable output) Logical, if TRUE the file is in landscape format.
By default: FALSE if style is 'report' and TRUE if style is 'presentation'.

(flextable output) Character vector with footer(s) for the table. Set to NULL (by default) if no footer should be included.

(flextable output) String mentioning how vertical lines should be included in the body of the table, either:

• 'none' (default): no vertical lines included

• 'auto': vertical lines included between sub-groups

(flextable output) String mentioning how horizontal lines should be included in the body of the table, either:

• 'none': no horizontal lines included

• 'auto' (default): horizontal lines included between sub-groups

String with path of the file where the table should be exported. The file should have the extension: '.html'. If NULL, the summary table is not exported but only returned as output. If byVar is specified, each table is exported to a separated file with the suffix: 'file_[i].html' with i the index of the file.

(flextable output) Logical, if TRUE (FALSE by default) the column header is merged.

Numeric vector.

Logical, should NA value(s) be removed (FALSE by default)?

Data.frame with data.

Character vector with variable(s) to consider.

(optional) Data.frame with data to consider to define the levels of the variable. If not specified, only the combinations of variable(s) available in the data are retained.

a flextable object

a data.frame specyfing for each colname content of the column.

Summary table as created internally in computeSummaryStatisticsTable.

Character vector, subset of var with variable(s) of type 'flag' (with 'Y', 'N' or ” for empty/non specified value). Only the counts for records flagged (with 'Y') are retained.

Numeric vector.

Logical, should NA value(s) be removed (FALSE by default)?

Integer vector with padding.

Data.frame with summary statistics to represent in the plot, e.g. a summaryTable object.

String, variable of data with variable for the x-axis.

String with label for the xVar.

Object passed to the 'expand' parameter of: scale_x_continuous, (waiver by default).

(optional) Numeric vector of length 2 for which a gap should be created in the x-axis. Only available if xVar is specified and a numeric variable. Records with xVar within xGap are filtered from the plot, vertical lines are included at the min/max of the gap, and the gap is represented as '//' in the x-axis of the plot.

Numeric vector of length 2 with new range of the xGap. If not specified, the minimum difference between consecutive x elements in the data is used.

String, variable of data with the mean variable.

String, variable of data with the standard error.

String, variables of data with minimum and maximum value for error bar. If both are specified, seVar is ignored.

String with label for the y-axis. If different labels should be used for different elements of byVar variable, the vector should be named with each corresponding element (collapsed with '.' if multiple).

Character vector, variable(s) of data for facetting.

String with type of scale used for facetting, 'free_y' by default (fixed scale in the x-axis and free in the y-axis).

String, variable of data for coloring.

String, label for colorVar, used in the legend.

(named) Vector with color palette.

Named string with variable labels (names are the variable code).

Logical, if TRUE (FALSE by default) use also linetype to differenciate the variable specified via colorVar in the mean line.

Vector with linetype(s), in case useLinetype is TRUE.

Logical, if TRUE (by default) colorVar is also used for the shape.

Named vector with shape palette for colorVar.

Numeric with jitter for the x-axis, only used if colorVar specified.

String with title for the plot. If different labels should be used for different elements of byVar variable, the vector should be named with each corresponding element (collapsed with '.' if multiple).

String with caption for the plot, NULL by default.

(optional) String with transformation for the y-axis. Currently only 'log10' (or NULL, default) is available. In case error bars go in the negative, their values are set to a 'small enough' value for plotting: min(data)/10 or yLim[1] if yLim is specified.

Vector of the length 2 with limits for the y-axis.

Vector of the length 2 with limits for the x-axis.

Expansion constants for the limits for the y-axis. See the documentation of the expand parameter of the scale_y_continuous function for the available values for this parameter.

This parameter is deprecated, use yAxisExpand instead.

(optional) Named character vector with labels for the x-axis.

Size for the point.

Size for the line linking means and error bars.

Size for the label, only used if label is not NULL.

Numeric vector of length 1 with width of error bar.

(optional) Character vector with colname of data or expression from colnames of data to be represented in the table below the plot. By default, no table is displayed.

Font face for the text included in the table.

Numeric of length 1 with height for the table.

Logical, if TRUE (by default) the labels of the colorVar are included in the y-axis of the table.

Margin between the plot and the table, expressed as unit, 0 by default.

Logical or expression or list of expression. Points are labelled with meanVar if set to TRUE, or with the specified expression if label is an expression. If a list is specified, 'textLabel' (required) should contain expression to extract label, and 'textHjust' and 'textVjust' (optional) may contain expression specifying horizontal and vertical adjustment of the label.

Amount of padding (space) between each point and its label, 1.5 lines by default. See parameter point.padding of the geom_text_repel function.

Variable(s) of data for which separated plot(s) should be created.

(optional) numeric with y-intercept of line(s) to be added. If different thresholds should be used for different elements of the byVar or facetVar variables, the vector should be named with each corresponding element (collapsed with '.' if multiple).

String with color for hLine, 'black' by default.

String with linetype for hLine, 'solid' by default.

(optional) numeric with x-intercept of line(s) to be added. If different thresholds should be used for different elements of the byVar or facetVar variables, the vector should be named with each corresponding element (collapsed with '.' if multiple).

String with color for vLine, 'black' by default.

String with linetype for vLine, 'solid' by defaul

String with subject profile style. This affects the parameters: fontname, fontsize and themeFct.

String with font name, by default 'Times' if style is 'report' and 'Tahoma' if style is 'presentation'.

Numeric vector of length 1 with font size, by default 8 if style is 'report' and 10 if style is 'presentation'

Function with ggplot2 theme, by default theme_classic if style is 'report' and theme_bw if style is 'presentation'.

Logical, if TRUE (by default) include theme vertical grid lines (if present in themeFct).

Extra ggplot call of function generating such call(s) to be added in main plot.
Multiple calls are set via a function, e.g. ggExtra = function(gg){gg + geom_vline(...) + geom_hline(...)}.
If different calls should be used for different elements of the byVar variable, the vector should be named with each corresponding element (collapsed with '.' if multiple).

String with legend position. By default, 'bottom' of tableText is not specified, 'none' otherwise.

Additional parameters for geom_text_repel or geom_text used for the label.

Data.frame (in long format) with data for the table.

String, variable of data with variable for the x-axis.

Character vector with colnames of data or expression based on colnames of data to extract the text label.

Vector of the length 2 with limits for the x-axis.

String, variable of data for coloring.

(named) Vector with color palette.

String, label for colorVar, used in the legend.

Numeric, fontface for the text.

String with label for the x-axis.

Named string with variable labels (names are the variable code).

String with caption for the plot, NULL by default.

Logical, should the legend be displayed? TRUE by default.

String with legendPosition, 'right' by default.

Logical, if TRUE include the labels in the y-axis.

Vector with labels for the x-axis if xVar is discrete or vector with limits if continuous.

String with subject profile style. This affects the parameters: fontname, fontsize and themeFct.

String with font name, by default 'Times' if style is 'report' and 'Tahoma' if style is 'presentation'.

Numeric vector of length 1 with font size, by default 8 if style is 'report' and 10 if style is 'presentation'

Numeric indicating the size of points in the legend, 1.5 by default

Function with ggplot2 theme, by default theme_classic if style is 'report' and theme_bw if style is 'presentation'.

Size for the text.

(optional) ggplot2 transformation for the x-axis.

Lists

Data.frame to export to the table, or list of such tables.

String with text file to export to.

Any parameters passed to the write.table function.