export.summaryTable {inTextSummaryTable}

Export a summary table to docx, pptx or html format (interactive table)

Description

The use of export is recommended.
exportSummaryStatisticsTable is retained for back-compatibility.

Usage

## S3 method for class 'summaryTable'
export(...)

exportSummaryStatisticsTable(
  summaryTable,
  rowVar = getAttribute(summaryTable, "rowVar"),
  rowVarLab = getAttribute(summaryTable, "rowVarLab", default = getLabelVar(rowVar,
    labelVars = labelVars)),
  rowVarInSepCol = NULL,
  rowVarFormat = NULL,
  rowVarTotalInclude = getAttribute(summaryTable, "rowVarTotalInclude"),
  rowTotalLab = NULL,
  rowVarTotalInSepRow = getAttribute(summaryTable, "rowVarTotalInSepRow"),
  rowAutoMerge = TRUE,
  colVar = getAttribute(summaryTable, "colVar"),
  colTotalLab = getAttribute(summaryTable, "colTotalLab", default = "Total"),
  colHeaderTotalInclude = TRUE,
  colHeaderMerge = TRUE,
  statsVar = getAttribute(summaryTable, "statsVar"),
  statsLayout = getAttribute(summaryTable, "statsLayout", default = ifelse("DT" %in%
    outputType, "col", "row")),
  statsValueLab = "StatisticValue",
  statsLabInclude = NULL,
  emptyValue = "-",
  labelVars = NULL,
  file = NULL,
  title = NULL,
  outputType = "flextable",
  pageDim = NULL,
  columnsWidth = NULL,
  landscape = (style == "presentation"),
  margin = 1,
  rowPadBase = 14.4,
  footer = NULL,
  style = "report",
  colorTable = getColorPaletteTable(style = style),
  fontsize = switch(style, report = 8, presentation = 10),
  fontname = switch(style, report = "Times", presentation = "Tahoma"),
  vline = "none",
  hline = "auto",
  expandVar = NULL,
  noEscapeVar = NULL,
  barVar = NULL,
  ...
)

Arguments

...

(DT output) Extra parameters passed to the getClinDT

summaryTable

A summaryTable object.

rowVar

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.

rowVarLab

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

rowVarInSepCol

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'.

rowVarFormat

(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.)

rowVarTotalInclude

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.

rowTotalLab

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

rowVarTotalInSepRow

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.

rowAutoMerge

(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.

colVar

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.

colTotalLab

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

colHeaderTotalInclude

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

colHeaderMerge

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

statsVar

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.

statsLayout

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)

statsValueLab

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.

statsLabInclude

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.

emptyValue

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.

labelVars

(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.

file

(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).

title

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).

outputType

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

pageDim

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))

columnsWidth

(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).

landscape

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

margin

(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].

rowPadBase

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

footer

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

style

(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.

colorTable

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

fontsize

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

fontname

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

vline

(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

hline

(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

expandVar

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

noEscapeVar

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

barVar

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

Value

Depending on the outputType:

• 'data.frame-base': input summary table in a long format with all computed statistics

• 'data.frame': summary table in a wide format ( different columns for each colVar), with specified labels

• 'flextable' (by default): flextable object with summary table

• 'DT': datatable object with summary table

If multiple outputType are specified, a list of those objects, named by outputType.
If byVar is specified, each object consists of a list of tables, one for each element in byVar.

Functions

• export(summaryTable): export summaryTable object

Author(s)

Laure Cougnaud