# Proportional hazards assumption: trouble interpreting my results for cox.zph() function in R

I am testing my proportional hazards assumption in R using the cox.zph() function:

library(survival)
km.fit1 <- survfit(Surv(Days[which(Site=="LP")],Status[which(Site=="LP")])~Treat[which(Site=="LP")],
data=data2, type="kaplan-meier")
coxph1 <- coxph(Surv(Days[which(Site=="LP")],Status[which(Site=="LP")])~Treat[which(Site=="LP")],
data=data2)

test <- cox.zph(coxph1)
test
rho chisq      p
Treat[which(Site == "LP")]WC -0.0495  1.55 0.2127
Treat[which(Site == "LP")]WO -0.0932  5.49 0.0191
GLOBAL                            NA  5.50 0.0640
par(mfrow=c(1,3))
plot(test)


My first problem is why does the output only show for treatments WC and WO and not for my third treatment, W?

My second problem is why when I plot(test) does it come up with two plots (one for WC and one for WO) even though I really only wanted to look at one plot (Treat) which is a 3 level factor (explained by the 3 horizontal lines)?.

• I'm voting to close this question as off-topic because the question is addressing programming in R. Mar 8, 2017 at 20:45
• The only problem that I have is with interpreting the results that I'm getting--not with the codes that I used Mar 8, 2017 at 21:00