Hello all:
I'm attempting to run a Cox proportional hazards function on survival data
from insects and I have a few questions.
My current command that I'm using to call the model is as follows (using
coxph() from the survival library):
coxph(Surv(day, censor) ~ treatment + room + chamber %in% treatment, data
data.table)
Day indicates which day a particular observation occurred, and censor indicates
the type of observation; that is, mortality or emergence.
My first question is: how do I code my censor variable? I am interested in
treatment effects on mortality, and the mortality observations are currently
coded as a 1 in the censor variable. Emergence is another mechanism by which
the insects in my study may leave the system, similar to a patient opting
out in the middle of a clinical study, and are coded as a 0.
I also have a nested and block variable that I'm unsure of how to deal with.
Chamber is nested within treatment, where each chamber has a maximum of 4
observations or insects, all within 1 treatment. The block variable is room,
where each room contains ~40 chambers each of which has been randomly
assigned a treatment. I believe that I have chamber %in% treatment right in
representing my data, but how do I account for room as a block?
Additionally, I have a frequency column in data.table that indicates how
many of a particular observation occurred in each row. Is it appropriate to
assign this column as a weigh argument in cosph? If so, how is that done?
I can send sample data if necessary. Thanks for any help!
Justin Montemarano
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