summary.pyears {survival}  R Documentation 
Summary function for pyears objecs
Description
Create a printable table of a personyears result.
Usage
## S3 method for class 'pyears'
summary(object, header = TRUE, call = header, n = TRUE,
event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, rr =expected,
ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vline = FALSE,
vertical= TRUE, nastring=".", conf.level = 0.95,
scale = 1, ...)
Arguments
object 
a pyears object 
header 
print out a header giving the total number of observations, events, personyears, and total time (if any) omitted from the table 
call 
print out a copy of the call 
n , event , pyears , expected 
logical arguments: should these elements be printed in the table? 
rate , ci.r 
logical arguments: should the incidence rate and/or its confidence interval be given in the table? 
rr , ci.rr 
logical arguments: should the hazard ratio and/or its confidence interval be given in the table? 
totals 
should row and column totals be added? 
legend 
should a legend be included in the printout? 
vline 
should vertical lines be included in the printed tables? 
vertical 
when there is only a single predictor, should the table be printed with the predictor on the left (vertical=TRUE) or across the top (vertical=FALSE)? 
nastring 
what to use for missing values in the table. Some of these are structural, e.g., risk ratios for a cell with no followup time. 
conf.level 
confidence level for any confidence intervals 
scale 
a scaling factor for printed rates 
... 
optional arguments which will be passed to the

Details
The pyears
function is often used to create initial
descriptions of a survival or timetoevent variable; the type of
material that is often found in “table 1” of a paper. The summary
routine prints this information out using one of pandoc table styles.
A primary reason for choosing this style is that Rstudio is then able
to automatically render the results in multiple formats: html, rtf,
latex, etc.
If the pyears
call has only a single covariate then the table
will have that covariate as one margin and the statistics of interest
as the other.
If the pyears
call has two predictors then those two predictors
are used as margins of the table, while each cell of the table
contains the statistics of interest as multiple rows within the cell.
If there are more than two predictors then multiple tables are
produced, in the same order as the standard R printout for an array.
The "N" entry of a pyears object is the number of observations which
contributed to a particular cell. When the original call includes
tcut
objects then a single observation may contribute to
multiple cells.
Value
a copy of the object
Notes
The pandoc system has four table types: with or without vertical bars, and with single or multiple rows of data in each cell. This routine produces all 4 styles depending on options, but currently not all of them are recognized by the Rstudiopandoc pipeline. (And we don't yet see why.)
Author(s)
Terry Therneau and Elizabeth Atkinson