library(knitr) opts_chunk$set( echo = TRUE, results = 'markup', warning = FALSE, # stop document execution if error (not the default) error = FALSE, message = FALSE, cache = FALSE, fig.width = 8, fig.height = 7, fig.path = "./figures_vignette/", fig.align = 'center') options(width = 170) # instead of warn = 0 by default # include warnings when they occur in the document options(warn = 1)
The package inTextSummaryTable
contains functionalities to create
complex table of summary statistics or counts of variables of interest.
This table can be formatted to static
These tables can be included into a rmarkdown
document which can be
converted into html
, docx
and pptx
.
Each table can be separately exported into a text
, docx
or html
document.
We start the guidance to the functionalities of the inTextSummaryTable
, via
loading the following packages.
library(inTextSummaryTable) library(pander) library(tools) # toTitleCase
The input data for the creation of summary table should be a data.frame,
usually loaded from a SAS data file (sas7bdat
format).
The label of the variables stored in the SAS
datasets is also used
for the title or the caption.
Note that the loadDataADaMSDTM
function of the clinUtils
package
can be used to import your study-specific dataset(s) of interest into R.
For this vignette, ADaM datasets included in the clinUtils
package are used.
library(clinUtils) # load example data data(dataADaMCDISCP01) dataAll <- dataADaMCDISCP01 labelVars <- attr(dataAll, "labelVars") # dataAll contains a list class(dataAll) # ... of ADaM datasets names(dataAll) # access a specific dataset head(dataAll$ADSL, 1) # check label of a subset of the variable(s) head(labelVars) # or for a specific variable: labelVars["USUBJID"] # or: getLabelVar(var = "USUBJID", labelVars = labelVars)
A dedicated vignette on how to create your in-text table is available here).
If you are familiar with the creation of the tables, but you are wondering how to:
then the the dedicated vignette is available here), or accessible with
vignette("inTextSummaryTable-exportTables", "inTextSummaryTable")
If you are familiar with the creation and export of the tables, and you want to know more on the functionalities less exposed to the users, you can check out the vignette for advanced users, which is available here) and with
vignette("inTextSummaryTable-advanced", "inTextSummaryTable")
The inTextSummaryTable
has also visualization functionalities based on the
computation of summary statistics. The vignette for visualization is available
at this) link or through
vignette("inTextSummaryTable-visualization", "inTextSummaryTable")
The inTextSummaryTable
package allow the user to set global options for the
color schemes of tables and visualization. The main advantage is that if
you wish to change the default palettes, it is possible to set your preferences
only once at the beginning of the R script or Rmd document.
The vignette is available via this) link or
vignette("inTextSummaryTable-aesthetics", "inTextSummaryTable")
pander(sessionInfo())
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