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Last data update: 2014.03.03

R: Performs Log Rank test on the long and short patient sets

logrnk

R Documentation

Performs Log Rank test on the long and short patient sets

Description

This function performs a Chi-square test on the long and short subject sets to determine if their is a significant difference between the survival times in both sets. It returns the p-value.

Usage

logrnk(dataL, dataS)

Arguments

`dataL`	The set of subjects predicted to fall into the long-survivor set. A data frame containing at least the following columns: “PatientOrderValidation” (the number/order of the subject); “group” (the group into which the patient falls L (for long) or S(for short)); “censored” (the censorship status of the patient $1$ for uncensored and $0$ for censored).
`dataS`	Same as “dataL” but for the set of short survivors.

Details

Note that the typical arguments to be passed are the results of the “STpredict” functions “long_survivors” and “long_survivors”

Value

The estimated p-value is returned

Author(s)

Douaa AS Mugahid

References

Bland JM, Altman DG. Survival probabilities (the Kaplan-Meier method). BMJ 2004;328;1073 http://www.bmj.com/statsbk/12.dtl

Examples

PatientOrderValidation_L <- c(1, 2, 3, 5, 7)
PatientOrderValidation_S <- c(4, 6, 8)
group_L <- rep("L", 5)
group_S <- rep("S", 3)
censored_L <- c(0, 0, 1, 1, 0)
censored_S <- c(0, 0, 1)
True_STs_L <- c(5, 6, 6 ,7, 8)
True_STs_S <- c(2, 3, 2)
short <- as.data.frame(cbind(PatientOrderValidation_S, group_S, censored_S, True_STs_S))
long <- as.data.frame(cbind(PatientOrderValidation_L, group_L, censored_L, True_STs_L))
names(short) <- c("PatientOrderValidation", "group", "censored", "True_STs")
names(long) <- c("PatientOrderValidation", "group", "censored", "True_STs")
logrnk(dataL=long, dataS=short)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(RCASPAR)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RCASPAR/logrnk.Rd_%03d_medium.png", width=480, height=480)
> ### Name: logrnk
> ### Title: Performs Log Rank test on the long and short patient sets
> ### Aliases: logrnk
> ### Keywords: log rank test
> 
> ### ** Examples
> 
> PatientOrderValidation_L <- c(1, 2, 3, 5, 7)
> PatientOrderValidation_S <- c(4, 6, 8)
> group_L <- rep("L", 5)
> group_S <- rep("S", 3)
> censored_L <- c(0, 0, 1, 1, 0)
> censored_S <- c(0, 0, 1)
> True_STs_L <- c(5, 6, 6 ,7, 8)
> True_STs_S <- c(2, 3, 2)
> short <- as.data.frame(cbind(PatientOrderValidation_S, group_S, censored_S, True_STs_S))
> long <- as.data.frame(cbind(PatientOrderValidation_L, group_L, censored_L, True_STs_L))
> names(short) <- c("PatientOrderValidation", "group", "censored", "True_STs")
> names(long) <- c("PatientOrderValidation", "group", "censored", "True_STs")
> logrnk(dataL=long, dataS=short)
$Xsq
[1] 1.5

$pValue
[1] 0.2206714

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>