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I am trying to plot a survival curve with interval censor data. I have been able to successfully plot the survival curve using the interval censor data (shown below), although I am not sure if I coded the events right, such as if I should even use 1?

Here is the code I used to generate the survival curve.

simafit <- survfit(Surv(Time1, Time2, Event, type = c('interval')) ~ 
Treatment, data = sima)

ggsurvplot(simafit, conf.int = TRUE, 
legend.labs=c("Control","Drought","Water+"), ggtheme = theme_bw(), 
legend.title = "Treatment", title ="Sidalcea malviflora", palette = 
c("gray47","orangered","deepskyblue"),xlim=c(0,838), ylim=c(0,1), xlab="Days 
Since Planting")+scale_x_continuous(expand = c(0, 0)) + 
scale_y_continuous(expand = c(0, 0))

survival plot

Next I am trying to use the survreg function to test for differences between treatments and get p-values.

Here is my code: 

survreg(Surv(Time1d, Time2d, Event, type = c('interval')) ~ Treatment,
        dist="weibull", data = sima)

but I keep getting the error:

    Error in survreg(Surv(Time1d, Time2d, Event, type = c("interval")) ~ Treatment,  : 
Invalid survival times for this distribution

I originally tried with Time1 and Time2 but then I read that 0s don't work in the function so I made an extra copy to test. I've tried presenting the data in many different ways but I can't find any that work with survreg but this format worked well with ggsurvplot , but maybe the format needs to be different for the two functions?

I'd appreciate any help, thanks ahead of time.

Here is the data:

    Plot ID Subplot Treatment   Column  Row Species Time1   Time2   Event   Time1d  Time2d
    PS1 1   shelter A   7   SIMA    Inf 0   0   1   1
    PS1 2   shelter C   2   SIMA    Inf 0   0   1   1
    PS1 3   shelter D   2   SIMA    Inf 0   0   1   1
    PS2 1   shelter A   7   SIMA    Inf 0   0   1   1
    PS2 2   shelter C   2   SIMA    Inf 0   0   1   1
    PS2 3   shelter D   2   SIMA    Inf 0   0   1   1
    PS3 1   shelter A   7   SIMA    Inf 0   0   1   1
    PS3 2   shelter C   2   SIMA    Inf 0   0   1   1
    PS3 3   shelter D   2   SIMA    Inf 0   0   1   1
    PS4 1   shelter A   7   SIMA    Inf 0   0   1   1
    PS4 2   shelter C   2   SIMA    Inf 0   0   1   1
    PS4 3   shelter D   2   SIMA    Inf 0   0   1   1
    PS5 1   shelter A   7   SIMA    Inf 0   0   1   1
    PS5 2   shelter C   2   SIMA    Inf 0   0   1   1
    PS5 3   shelter D   2   SIMA    Inf 0   0   1   1
    PC1 1   control A   7   SIMA    Inf 0   0   1   1
    PC1 2   control C   2   SIMA    Inf 0   0   1   1
    PC1 3   control D   2   SIMA    Inf 0   0   1   1
    PC2 1   control A   7   SIMA    Inf 0   0   1   1
    PC2 2   control C   2   SIMA    Inf 0   0   1   1
    PC2 3   control D   2   SIMA    Inf 0   0   1   1
    PC3 1   control A   7   SIMA    Inf 0   0   1   1
    PC3 2   control C   2   SIMA    Inf 0   0   1   1
    PC3 3   control D   2   SIMA    Inf 0   0   1   1
    PC4 1   control A   7   SIMA    Inf 0   0   1   1
    PC4 2   control C   2   SIMA    Inf 0   0   1   1
    PC4 3   control D   2   SIMA    Inf 0   0   1   1
    PC5 1   control A   7   SIMA    Inf 0   0   1   1
    PC5 2   control C   2   SIMA    Inf 0   0   1   1
    PC5 3   control D   2   SIMA    Inf 0   0   1   1
    PW1 1   watered A   7   SIMA    Inf 0   0   1   1
    PW1 2   watered C   2   SIMA    Inf 0   0   1   1
    PW1 3   watered D   2   SIMA    Inf 0   0   1   1
    PW2 1   watered A   7   SIMA    Inf 0   0   1   1
    PW2 2   watered C   2   SIMA    Inf 0   0   1   1
    PW2 3   watered D   2   SIMA    Inf 0   0   1   1
    PW3 1   watered A   7   SIMA    Inf 0   0   1   1
    PW3 2   watered C   2   SIMA    Inf 0   0   1   1
    PW3 3   watered D   2   SIMA    Inf 0   0   1   1
    PW4 1   watered A   7   SIMA    Inf 0   0   1   1
    PW4 2   watered C   2   SIMA    Inf 0   0   1   1
    PW4 3   watered D   2   SIMA    Inf 0   0   1   1
    PW5 1   watered A   7   SIMA    Inf 0   0   1   1
    PW5 2   watered C   2   SIMA    Inf 0   0   1   1
    PW5 3   watered D   2   SIMA    Inf 0   0   1   1
    PS1 1   shelter A   7   SIMA    0   26  0   1   26
    PS1 2   shelter C   2   SIMA    0   26  0   1   26
    PS1 3   shelter D   2   SIMA    0   26  0   1   26
    PS2 1   shelter A   7   SIMA    0   26  0   1   26
    PS2 2   shelter C   2   SIMA    0   26  0   1   26
    PS2 3   shelter D   2   SIMA    0   26  0   1   26
    PS3 1   shelter A   7   SIMA    0   26  0   1   26
    PS3 2   shelter C   2   SIMA    0   26  0   1   26
    PS3 3   shelter D   2   SIMA    0   26  0   1   26
    PS4 1   shelter A   7   SIMA    0   26  0   1   26
    PS4 2   shelter C   2   SIMA    0   26  0   1   26
    PS4 3   shelter D   2   SIMA    0   26  0   1   26
    PS5 1   shelter A   7   SIMA    0   26  0   1   26
    PS5 2   shelter C   2   SIMA    0   26  0   1   26
    PS5 3   shelter D   2   SIMA    0   26  0   1   26
    PC1 1   control A   7   SIMA    0   26  0   1   26
    PC1 2   control C   2   SIMA    0   26  0   1   26
    PC1 3   control D   2   SIMA    0   26  0   1   26
    PC2 1   control A   7   SIMA    0   26  0   1   26
    PC2 2   control C   2   SIMA    0   26  0   1   26
    PC2 3   control D   2   SIMA    0   26  0   1   26
    PC3 1   control A   7   SIMA    0   26  0   1   26
    PC3 2   control C   2   SIMA    0   26  0   1   26
    PC3 3   control D   2   SIMA    0   26  0   1   26
    PC4 1   control A   7   SIMA    0   26  0   1   26
    PC4 2   control C   2   SIMA    0   26  0   1   26
    PC4 3   control D   2   SIMA    0   26  0   1   26
    PC5 1   control A   7   SIMA    0   26  1   1   26
    PC5 2   control C   2   SIMA    0   26  0   1   26
    PC5 3   control D   2   SIMA    0   26  0   1   26
    PW1 1   watered A   7   SIMA    0   26  0   1   26
    PW1 2   watered C   2   SIMA    0   26  0   1   26
    PW1 3   watered D   2   SIMA    0   26  0   1   26
    PW2 1   watered A   7   SIMA    0   26  0   1   26
    PW2 2   watered C   2   SIMA    0   26  0   1   26
    PW2 3   watered D   2   SIMA    0   26  0   1   26
    PW3 1   watered A   7   SIMA    0   26  0   1   26
    PW3 2   watered C   2   SIMA    0   26  0   1   26
    PW3 3   watered D   2   SIMA    0   26  0   1   26
    PW4 1   watered A   7   SIMA    0   26  0   1   26
    PW4 2   watered C   2   SIMA    0   26  0   1   26
    PW4 3   watered D   2   SIMA    0   26  0   1   26
    PW5 1   watered A   7   SIMA    0   26  0   1   26
    PW5 2   watered C   2   SIMA    0   26  0   1   26
    PW5 3   watered D   2   SIMA    0   26  0   1   26
    PS1 1   shelter A   7   SIMA    26  92  0   26  92
    PS1 2   shelter C   2   SIMA    26  92  0   26  92
    PS1 3   shelter D   2   SIMA    26  92  0   26  92
    PS2 1   shelter A   7   SIMA    26  92  0   26  92
    PS2 2   shelter C   2   SIMA    26  92  0   26  92
    PS2 3   shelter D   2   SIMA    26  92  0   26  92
    PS3 1   shelter A   7   SIMA    26  92  0   26  92
    PS3 2   shelter C   2   SIMA    26  92  0   26  92
    PS3 3   shelter D   2   SIMA    26  92  0   26  92
    PS4 1   shelter A   7   SIMA    26  92  0   26  92
    PS4 2   shelter C   2   SIMA    26  92  0   26  92
    PS4 3   shelter D   2   SIMA    26  92  0   26  92
    PS5 1   shelter A   7   SIMA    26  92  0   26  92
    PS5 2   shelter C   2   SIMA    26  92  0   26  92
    PS5 3   shelter D   2   SIMA    26  92  0   26  92
    PC1 1   control A   7   SIMA    26  92  0   26  92
    PC1 2   control C   2   SIMA    26  92  0   26  92
    PC1 3   control D   2   SIMA    26  92  0   26  92
    PC2 1   control A   7   SIMA    26  92  0   26  92
    PC2 2   control C   2   SIMA    26  92  0   26  92
    PC2 3   control D   2   SIMA    26  92  0   26  92
    PC3 1   control A   7   SIMA    26  92  0   26  92
    PC3 2   control C   2   SIMA    26  92  0   26  92
    PC4 1   control A   7   SIMA    26  92  0   26  92
    PC4 2   control C   2   SIMA    26  92  0   26  92
    PC4 3   control D   2   SIMA    26  92  0   26  92
    PC5 1   control A   7   SIMA    26  92  3   26  92
    PC5 2   control C   2   SIMA    26  92  0   26  92
    PC5 3   control D   2   SIMA    26  92  0   26  92
    PW1 1   watered A   7   SIMA    26  92  0   26  92
    PW1 2   watered C   2   SIMA    26  92  0   26  92
    PW1 3   watered D   2   SIMA    26  92  0   26  92
    PW2 1   watered A   7   SIMA    26  92  0   26  92
    PW2 2   watered C   2   SIMA    26  92  0   26  92
    PW2 3   watered D   2   SIMA    26  92  0   26  92
    PW3 1   watered A   7   SIMA    26  92  0   26  92
    PW3 2   watered C   2   SIMA    26  92  0   26  92
    PW3 3   watered D   2   SIMA    26  92  0   26  92
    PW4 1   watered A   7   SIMA    26  92  0   26  92
    PW4 2   watered C   2   SIMA    26  92  0   26  92
    PW4 3   watered D   2   SIMA    26  92  0   26  92
    PW5 1   watered A   7   SIMA    26  92  0   26  92
    PW5 2   watered C   2   SIMA    26  92  0   26  92
    PW5 3   watered D   2   SIMA    26  92  0   26  92
    PS1 1   shelter A   7   SIMA    92  120 0   92  120
    PS1 2   shelter C   2   SIMA    92  120 0   92  120
    PS1 3   shelter D   2   SIMA    92  120 0   92  120
    PS2 1   shelter A   7   SIMA    92  120 0   92  120
    PS2 2   shelter C   2   SIMA    92  120 0   92  120
    PS2 3   shelter D   2   SIMA    92  120 0   92  120
    PS3 1   shelter A   7   SIMA    92  120 0   92  120
    PS3 2   shelter C   2   SIMA    92  120 0   92  120
    PS3 3   shelter D   2   SIMA    92  120 0   92  120
    PS4 1   shelter A   7   SIMA    92  120 0   92  120
    PS4 2   shelter C   2   SIMA    92  120 0   92  120
    PS4 3   shelter D   2   SIMA    92  120 0   92  120
    PS5 1   shelter A   7   SIMA    92  120 0   92  120
    PS5 2   shelter C   2   SIMA    92  120 0   92  120
    PS5 3   shelter D   2   SIMA    92  120 0   92  120
    PC1 1   control A   7   SIMA    92  120 0   92  120
    PC1 2   control C   2   SIMA    92  120 0   92  120
    PC1 3   control D   2   SIMA    92  120 0   92  120
    PC2 1   control A   7   SIMA    92  120 0   92  120
    PC2 2   control C   2   SIMA    92  120 0   92  120
    PC2 3   control D   2   SIMA    92  120 0   92  120
    PC3 1   control A   7   SIMA    92  120 0   92  120
    PC3 2   control C   2   SIMA    92  120 0   92  120
    PC3 3   control D   2   SIMA    92  120 0   92  120
    PC4 1   control A   7   SIMA    92  120 0   92  120
    PC4 2   control C   2   SIMA    92  120 1   92  120
    PC4 3   control D   2   SIMA    92  120 1   92  120
    PC5 1   control A   7   SIMA    92  120 2   92  120
    PC5 2   control C   2   SIMA    92  120 0   92  120
    PC5 3   control D   2   SIMA    92  120 0   92  120
    PW1 1   watered A   7   SIMA    92  120 0   92  120
    PW1 2   watered C   2   SIMA    92  120 0   92  120
    PW1 3   watered D   2   SIMA    92  120 0   92  120
    PW2 1   watered A   7   SIMA    92  120 0   92  120
    PW2 2   watered C   2   SIMA    92  120 0   92  120
    PW2 3   watered D   2   SIMA    92  120 0   92  120
    PW3 1   watered A   7   SIMA    92  120 0   92  120
    PW3 2   watered C   2   SIMA    92  120 1   92  120
    PW3 3   watered D   2   SIMA    92  120 0   92  120
    PW4 1   watered A   7   SIMA    92  120 1   92  120
    PW4 2   watered C   2   SIMA    92  120 0   92  120
    PW4 3   watered D   2   SIMA    92  120 0   92  120
    PW5 1   watered A   7   SIMA    92  120 0   92  120
    PW5 2   watered C   2   SIMA    92  120 0   92  120
    PW5 3   watered D   2   SIMA    92  120 0   92  120
    PS1 1   shelter A   7   SIMA    120 152 0   120 152
    PS1 2   shelter C   2   SIMA    120 152 0   120 152
    PS1 3   shelter D   2   SIMA    120 152 0   120 152
    PS2 1   shelter A   7   SIMA    120 152 0   120 152
    PS2 2   shelter C   2   SIMA    120 152 0   120 152
    PS2 3   shelter D   2   SIMA    120 152 0   120 152
    PS3 1   shelter A   7   SIMA    120 152 0   120 152
    PS3 2   shelter C   2   SIMA    120 152 1   120 152
    PS3 3   shelter D   2   SIMA    120 152 0   120 152
    PS4 1   shelter A   7   SIMA    120 152 0   120 152
    PS4 2   shelter C   2   SIMA    120 152 0   120 152
    PS4 3   shelter D   2   SIMA    120 152 0   120 152
    PS5 1   shelter A   7   SIMA    120 152 1   120 152
    PS5 2   shelter C   2   SIMA    120 152 0   120 152
    PS5 3   shelter D   2   SIMA    120 152 0   120 152
    PC1 1   control A   7   SIMA    120 152 0   120 152
    PC1 2   control C   2   SIMA    120 152 0   120 152
    PC1 3   control D   2   SIMA    120 152 0   120 152
    PC2 1   control A   7   SIMA    120 152 0   120 152
    PC2 2   control C   2   SIMA    120 152 0   120 152
    PC2 3   control D   2   SIMA    120 152 0   120 152
    PC3 1   control A   7   SIMA    120 152 1   120 152
    PC3 2   control C   2   SIMA    120 152 1   120 152
    PC3 3   control D   2   SIMA    120 152 1   120 152
    PC4 1   control A   7   SIMA    120 152 1   120 152
    PC4 2   control C   2   SIMA    120 152 3   120 152
    PC4 3   control D   2   SIMA    120 152 3   120 152
    PC5 1   control A   7   SIMA    120 152 2   120 152
    PC5 2   control C   2   SIMA    120 152 1   120 152
    PC5 3   control D   2   SIMA    120 152 0   120 152
    PW1 1   watered A   7   SIMA    120 152 0   120 152
    PW1 2   watered C   2   SIMA    120 152 0   120 152
    PW1 3   watered D   2   SIMA    120 152 0   120 152
    PW2 1   watered A   7   SIMA    120 152 0   120 152
    PW2 2   watered C   2   SIMA    120 152 0   120 152
    PW2 3   watered D   2   SIMA    120 152 0   120 152
    PW3 1   watered A   7   SIMA    120 152 1   120 152
    PW3 2   watered C   2   SIMA    120 152 3   120 152
    PW3 3   watered D   2   SIMA    120 152 1   120 152
    PW4 1   watered A   7   SIMA    120 152 3   120 152
    PW4 2   watered C   2   SIMA    120 152 0   120 152
    PW4 3   watered D   2   SIMA    120 152 1   120 152
    PW5 1   watered A   7   SIMA    120 152 0   120 152
    PW5 2   watered C   2   SIMA    120 152 0   120 152
    PW5 3   watered D   2   SIMA    120 152 0   120 152
    PS1 1   shelter A   7   SIMA    152 535 0   152 535
    PS1 2   shelter C   2   SIMA    152 535 0   152 535
    PS1 3   shelter D   2   SIMA    152 535 0   152 535
    PS2 1   shelter A   7   SIMA    152 535 0   152 535
    PS2 2   shelter C   2   SIMA    152 535 0   152 535
    PS2 3   shelter D   2   SIMA    152 535 0   152 535
    PS3 1   shelter A   7   SIMA    152 535 0   152 535
    PS3 2   shelter C   2   SIMA    152 535 3   152 535
    PS3 3   shelter D   2   SIMA    152 535 0   152 535
    PS4 1   shelter A   7   SIMA    152 535 0   152 535
    PS4 2   shelter C   2   SIMA    152 535 1   152 535
    PS4 3   shelter D   2   SIMA    152 535 0   152 535
    PS5 1   shelter A   7   SIMA    152 535 0   152 535
    PS5 2   shelter C   2   SIMA    152 535 1   152 535
    PS5 3   shelter D   2   SIMA    152 535 1   152 535
    PC1 1   control A   7   SIMA    152 535 1   152 535
    PC1 2   control C   2   SIMA    152 535 0   152 535
    PC1 3   control D   2   SIMA    152 535 1   152 535
    PC2 1   control A   7   SIMA    152 535 0   152 535
    PC2 2   control C   2   SIMA    152 535 0   152 535
    PC2 3   control D   2   SIMA    152 535 1   152 535
    PC3 1   control A   7   SIMA    152 535 3   152 535
    PC3 2   control C   2   SIMA    152 535 0   152 535
    PC3 3   control D   2   SIMA    152 535 0   152 535
    PC4 1   control A   7   SIMA    152 535 3   152 535
    PC4 2   control C   2   SIMA    152 535 2   152 535
    PC4 3   control D   2   SIMA    152 535 2   152 535
    PC5 1   control A   7   SIMA    152 535 2   152 535
    PC5 2   control C   2   SIMA    152 535 3   152 535
    PC5 3   control D   2   SIMA    152 535 0   152 535
    PW1 1   watered A   7   SIMA    152 535 0   152 535
    PW1 2   watered C   2   SIMA    152 535 0   152 535
    PW1 3   watered D   2   SIMA    152 535 0   152 535
    PW2 1   watered A   7   SIMA    152 535 0   152 535
    PW2 2   watered C   2   SIMA    152 535 0   152 535
    PW2 3   watered D   2   SIMA    152 535 0   152 535
    PW3 1   watered A   7   SIMA    152 535 3   152 535
    PW3 2   watered C   2   SIMA    152 535 2   152 535
    PW3 3   watered D   2   SIMA    152 535 3   152 535
    PW4 1   watered A   7   SIMA    152 535 2   152 535
    PW4 2   watered C   2   SIMA    152 535 0   152 535
    PW4 3   watered D   2   SIMA    152 535 3   152 535
    PW5 1   watered A   7   SIMA    152 535 0   152 535
    PW5 2   watered C   2   SIMA    152 535 1   152 535
    PW5 3   watered D   2   SIMA    152 535 0   152 535
    PS1 1   shelter A   7   SIMA    535 829 0   535 829
    PS1 2   shelter C   2   SIMA    535 829 1   535 829
    PS1 3   shelter D   2   SIMA    535 829 0   535 829
    PS2 1   shelter A   7   SIMA    535 829 0   535 829
    PS2 2   shelter C   2   SIMA    535 829 0   535 829
    PS2 3   shelter D   2   SIMA    535 829 0   535 829
    PS3 1   shelter A   7   SIMA    535 829 0   535 829
    PS3 2   shelter C   2   SIMA    535 829 0   535 829
    PS3 3   shelter D   2   SIMA    535 829 0   535 829
    PS4 1   shelter A   7   SIMA    535 829 0   535 829
    PS4 2   shelter C   2   SIMA    535 829 3   535 829
    PS4 3   shelter D   2   SIMA    535 829 0   535 829
    PS5 1   shelter A   7   SIMA    535 829 0   535 829
    PS5 2   shelter C   2   SIMA    535 829 0   535 829
    PS5 3   shelter D   2   SIMA    535 829 0   535 829
    PC1 1   control A   7   SIMA    535 829 3   535 829
    PC1 2   control C   2   SIMA    535 829 0   535 829
    PC1 3   control D   2   SIMA    535 829 3   535 829
    PC2 1   control A   7   SIMA    535 829 0   535 829
    PC2 2   control C   2   SIMA    535 829 1   535 829
    PC2 3   control D   2   SIMA    535 829 3   535 829
    PC3 1   control A   7   SIMA    535 829 2   535 829
    PC3 2   control C   2   SIMA    535 829 0   535 829
    PC3 3   control D   2   SIMA    535 829 0   535 829
    PC4 1   control A   7   SIMA    535 829 2   535 829
    PC4 2   control C   2   SIMA    535 829 2   535 829
    PC4 3   control D   2   SIMA    535 829 2   535 829
    PC5 1   control A   7   SIMA    535 829 2   535 829
    PC5 2   control C   2   SIMA    535 829 2   535 829
    PC5 3   control D   2   SIMA    535 829 1   535 829
    PW1 1   watered A   7   SIMA    535 829 1   535 829
    PW1 2   watered C   2   SIMA    535 829 0   535 829
    PW1 3   watered D   2   SIMA    535 829 0   535 829
    PW2 1   watered A   7   SIMA    535 829 0   535 829
    PW2 2   watered C   2   SIMA    535 829 0   535 829
    PW2 3   watered D   2   SIMA    535 829 1   535 829
    PW3 1   watered A   7   SIMA    535 829 0   535 829
    PW3 2   watered C   2   SIMA    535 829 2   535 829
    PW3 3   watered D   2   SIMA    535 829 0   535 829
    PW4 1   watered A   7   SIMA    535 829 2   535 829
    PW4 2   watered C   2   SIMA    535 829 1   535 829
    PW4 3   watered D   2   SIMA    535 829 2   535 829
    PW5 1   watered A   7   SIMA    535 829 1   535 829
    PW5 2   watered C   2   SIMA    535 829 0   535 829
    PW5 3   watered D   2   SIMA    535 829 0   535 829
    PS1 1   shelter A   7   SIMA    829 Inf 0   829 Inf
    PS1 2   shelter C   2   SIMA    829 Inf 3   829 Inf
    PS1 3   shelter D   2   SIMA    829 Inf 0   829 Inf
    PS2 1   shelter A   7   SIMA    829 Inf 0   829 Inf
    PS2 2   shelter C   2   SIMA    829 Inf 0   829 Inf
    PS2 3   shelter D   2   SIMA    829 Inf 0   829 Inf
    PS3 1   shelter A   7   SIMA    829 Inf 0   829 Inf
    PS3 2   shelter C   2   SIMA    829 Inf 0   829 Inf
    PS3 3   shelter D   2   SIMA    829 Inf 0   829 Inf
    PS4 1   shelter A   7   SIMA    829 Inf 0   829 Inf
    PS4 2   shelter C   2   SIMA    829 Inf 2   829 Inf
    PS4 3   shelter D   2   SIMA    829 Inf 0   829 Inf
    PS5 1   shelter A   7   SIMA    829 Inf 0   829 Inf
    PS5 2   shelter C   2   SIMA    829 Inf 0   829 Inf
    PS5 3   shelter D   2   SIMA    829 Inf 0   829 Inf
    PC1 1   control A   7   SIMA    829 Inf 2   829 Inf
    PC1 2   control C   2   SIMA    829 Inf 0   829 Inf
    PC1 3   control D   2   SIMA    829 Inf 2   829 Inf
    PC2 1   control A   7   SIMA    829 Inf 0   829 Inf
    PC2 2   control C   2   SIMA    829 Inf 3   829 Inf
    PC2 3   control D   2   SIMA    829 Inf 2   829 Inf
    PC3 1   control A   7   SIMA    829 Inf 2   829 Inf
    PC3 2   control C   2   SIMA    829 Inf 0   829 Inf
    PC3 3   control D   2   SIMA    829 Inf 0   829 Inf
    PC4 1   control A   7   SIMA    829 Inf 2   829 Inf
    PC4 2   control C   2   SIMA    829 Inf 2   829 Inf
    PC4 3   control D   2   SIMA    829 Inf 2   829 Inf
    PC5 1   control A   7   SIMA    829 Inf 2   829 Inf
    PC5 2   control C   2   SIMA    829 Inf 2   829 Inf
    PC5 3   control D   2   SIMA    829 Inf 3   829 Inf
    PW1 1   watered A   7   SIMA    829 Inf 3   829 Inf
    PW1 2   watered C   2   SIMA    829 Inf 0   829 Inf
    PW1 3   watered D   2   SIMA    829 Inf 0   829 Inf
    PW2 1   watered A   7   SIMA    829 Inf 0   829 Inf
    PW2 2   watered C   2   SIMA    829 Inf 0   829 Inf
    PW2 3   watered D   2   SIMA    829 Inf 3   829 Inf
    PW3 1   watered A   7   SIMA    829 Inf 0   829 Inf
    PW3 2   watered C   2   SIMA    829 Inf 2   829 Inf
    PW3 3   watered D   2   SIMA    829 Inf 0   829 Inf
    PW4 1   watered A   7   SIMA    829 Inf 2   829 Inf
    PW4 2   watered C   2   SIMA    829 Inf 3   829 Inf
    PW4 3   watered D   2   SIMA    829 Inf 2   829 Inf
    PW5 1   watered A   7   SIMA    829 Inf 3   829 Inf
    PW5 2   watered C   2   SIMA    829 Inf 0   829 Inf
    PW5 3   watered D   2   SIMA    829 Inf 0   829 Inf

UPDATE

Ok per the comments and more background research I found that I could actually represent the data as right censored data:

    Plot ID Subplot Treatment   Column  Row Species Time    Event
    PS1 1   shelter A   7   SIMA    829 0
    PS1 2   shelter C   2   SIMA    829 1
    PS1 3   shelter D   2   SIMA    829 0
    PS2 1   shelter A   7   SIMA    829 0
    PS2 2   shelter C   2   SIMA    829 0
    PS2 3   shelter D   2   SIMA    829 0
    PS3 1   shelter A   7   SIMA    829 0
    PS3 2   shelter C   2   SIMA    829 0
    PS3 3   shelter D   2   SIMA    829 0
    PS4 1   shelter A   7   SIMA    829 0
    PS4 2   shelter C   2   SIMA    535 1
    PS4 3   shelter D   2   SIMA    829 0
    PS5 1   shelter A   7   SIMA    829 0
    PS5 2   shelter C   2   SIMA    829 0
    PS5 3   shelter D   2   SIMA    829 0
    PC1 1   control A   7   SIMA    535 1
    PC1 2   control C   2   SIMA    829 0
    PC1 3   control D   2   SIMA    535 1
    PC2 1   control A   7   SIMA    829 0
    PC2 2   control C   2   SIMA    829 1
    PC2 3   control D   2   SIMA    535 1
    PC3 1   control A   7   SIMA    152 1
    PC3 2   control C   2   SIMA    829 0
    PC3 3   control D   2   SIMA    829 0
    PC4 1   control A   7   SIMA    152 1
    PC4 2   control C   2   SIMA    120 1
    PC4 3   control D   2   SIMA    120 1
    PC5 1   control A   7   SIMA    92  1
    PC5 2   control C   2   SIMA    152 1
    PC5 3   control D   2   SIMA    829 1
    PW1 1   watered A   7   SIMA    829 1
    PW1 2   watered C   2   SIMA    829 0
    PW1 3   watered D   2   SIMA    829 0
    PW2 1   watered A   7   SIMA    829 0
    PW2 2   watered C   2   SIMA    829 0
    PW2 3   watered D   2   SIMA    829 1
    PW3 1   watered A   7   SIMA    829 0
    PW3 2   watered C   2   SIMA    120 1
    PW3 3   watered D   2   SIMA    829 0
    PW4 1   watered A   7   SIMA    120 1
    PW4 2   watered C   2   SIMA    829 1
    PW4 3   watered D   2   SIMA    152 1
    PW5 1   watered A   7   SIMA    829 1
    PW5 2   watered C   2   SIMA    535 1
    PW5 3   watered D   2   SIMA    829 0

Which I then applied this code to:

    rsimafit <- survfit(Surv(Time, Event, type = c('right')) ~ Treatment, data = rsima)

    ggsurvplot(rsimafit, conf.int = TRUE, pval = TRUE, legend.labs=c("Control","Drought","Water+"), ggtheme = theme_bw(), legend.title = "Treatment", title ="Sidalcea malviflora", palette = c("gray47","orangered","deepskyblue"),xlim=c(0,838), ylim=c(0,1), xlab="Days Since Planting")

I got this output: right censored plot

Now my biggest question is deciding upon which is the most appropriate model to use: survdiff survreg or coxph

I have done some background research but I do not have a strong background in statistical models or programming - from what I can tell: survreg is parametric survdiff is nonparametric coxph is semiparametric (not sure what that means) for testing multiple treatments and there interactions. Further, they all output similar p-values

I think all of these use some type of log-rank test to compare against a null hypothesis, which in my case would be control? Further I can't figure if post-hoc pairwise comparisons are feasible or appropriate in this situation. Any input or guidance would be appreciated. I have read many other examples on stackoverflow, statsexchange and crossvalidated, but am still stumped.

Justin Luong
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  • Why would it be meaningful to have a 0 survival time. – IRTFM Sep 03 '18 at 22:19
  • I have the data formatted as an interval censor set because I don't know the exact time of event, but I know it occurs between two monitoring periods. I put zero, as day zero of planting or the start date, but I guess 1 would make more sense. However I have tried with that as well and it doesn't seem to work – Justin Luong Sep 03 '18 at 23:31
  • You seem to be missing the point of my question. If Time1 and Time2 are both 0 then the difference would be the survival time in that strata and would be 0. Changing them both to 1 would not change that concern. – IRTFM Sep 03 '18 at 23:35
  • Indeed, you should have that Time2 > Time1 for all the rows in your dataset. – Dimitris Rizopoulos Sep 04 '18 at 04:42
  • Thanks for your comments, I have looked more into it and reformatted the data (editted into the original post) and it seems to work perfectly and now I can also do further tests that I wanted to do, but I am having a hard time deciding which is the best to use because the manual that comes with the package is pretty minimal - can anyone help me on this front? - Can post all three function outputs also if that is easier. – Justin Luong Sep 04 '18 at 18:05

1 Answers1

2

Function survreg() from the survival package fits parameteric accelerated failure time (AFT) models. AFT models are the analogue of simple linear regression applied to survival times (actually the log survival times), and accounting for censoring in the estimation. Because these are parametric models, indeed when you use them you’re making an assumption for the distribution of your survival times.

Function coxph() fits the semi-parametric Cox proportional hazards model. This is a model for the hazard function, and assumes a multiplicative effect of the covariates in the hazard scale. This models does not assume any particular distribution for your survival times, but it does make the proportional hazards assumption (i.e., the effect of covariates in the hazard scale is constant over time).

Function survdiff() perorms the log-rank test, and the Gehan-Wilcoxon test (if you set argument rho to 1). These tests test if the distribution of survival times of specific groups (e.g., males vs females) are equal. The log-rank test is equivalent to score test of a Cox model in which you including the group variable as a covariate.

Dimitris Rizopoulos
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  • Thanks Dimitris, one question I still have is if the parametric tests are appropriate if I have more than 2 groups or treatments? Can I make any pairwise comparison in treatments with them or will their output only tell me about overall survival of each group compared to the null hypothesis (they all have the same expected outcome)? Or in that case will only the cox proportional hazard model be appropriate? – Justin Luong Sep 05 '18 at 21:34
  • Yes, in both the parametric AFT model and the Cox PH model you can include a categorical group covariate with more than 2 categories/groups. Yes, you could also do pair wise comparisons using, e.g., package multcomp. – Dimitris Rizopoulos Sep 06 '18 at 06:42