JS.uni_fdr: A complete table for univariable survival analysis (C index,...

In SophiaJia/Jsurvformat: Survival analysis output format for clinical research

Description

JS.uni output the table with general multivariable survival analysis result with Number of total patients, Number of Events, HR (95% Confidence Interval),P value, C index and D index. This function only change the format of the output table. Note: c index and d index are from package survcomp.

Usage

JS.uni_fdr(Data, Event, Stime, Svar, groupn, Cat = F, cindex = F,
  dindex = F, AIC = F)

Arguments

Event	The status indicator, normally 0=alive, 1=dead
Stime	This is the follow up time
Svar	A vector of group
groupn	A text vector of the the group name for output
Cat	logical, indicating whether or not Svar is a categorical varaible
cindex	logical, indicating whether or not cindex should be in the table
dindex	logical, indicating whether or not dindex should be in the table
AIC	logical, indicating whether or not AIC should be in the table
D	A data.frame in which to interpret the variables

Value

A dataframe of coxph output including Number of total patients, Number of Events, HRs (95% Confidence Intervals), P values, C index and D index.

Examples

JS.uni_fdr(D = D ,"pd_censor", "pd_surv" , "tr_group", "Treatment" , Cat = T , cindex = F, dindex = F, AIC = F)

rtf output
rtf<-RTF("Table_survival.doc",width = 8.5, height = 11, font.size = 10, omi = c(1,1,1,1))
addHeader(rtf,title="Table , Survival Analysis  ")
addTable(rtf,isup_m.surv, font.size = 10, row.names = F, NA.string="-", col.widths = c(rep(0.6, 3), 2, rep(0.6, 3) ) )
done(rtf))

Rmarkdown output
save(isup_m.surv, file='myfile.Rda')

Then open at markdown file
library(knitr)
load("H:/Projects/myfile.Rda")
"```{r, echo=FALSE,results = 'asis'}"
output <- load("H:/Projects/p_Smith, Mitchell/Rituxan/Rituxan/T_BMI.Rdata")
knitr::kable(isup_m.surv, format = "markdown")  

SophiaJia/Jsurvformat documentation built on May 9, 2019, 1:52 p.m.