Ggtcf

I am new to Rmark and have spent the last several weeks exploring forums and manuals attempting to adapt code to my needs with little success.

I am using known-fate models within Rmark to try and relate vegetation covariates (taken over the course of 1 to 70 days) to the survival of the individuals (I'm curious if certain vegetation characteristics influence survival).

Currently my data is set up as follows (I'm showing a very abbreviated form, the real data has 70 rows-one for each individual- and contains more columns for additional covariates.

ch represents the known fate character string. It is 140 characters long relating to the 70 day period (format: observation,fate). g.1, f.1, s.1 are my covariates where the letter (i.e. "g") represents the variable and the #(ie 1) represents the time(day #) of the variable. So g.1 represents grass for day one, f.2 represents forb for day 2, etc. These columns go from g.1, f.1, s.1 all the way to g.70, f.70, s.70. From reading forums it seems this is the best way to format it since each individual needs it's own line.

Some individuals have values for all 70 days, however, most only have data for the first few days since they did not survive very long (we only recorded data if the individual was still alive). So, if an individual only survived 3 days, I would have values for g.1, f.1, s.1 through g.3, f.3, s.3, but g.4, f.4, s.4 through g.70,f.70, s.70 would all contain NA (which I'm sure will be an issue since I had to remove NA's to run survival models related to non-time varying covariates).

I have successfully ran survival models for non-time varying covariates (ie. weight), but I am unsure how to tackle this vegetation by time issue past the point which I am at. I have the standard known fate Rmark code (from example "blackduck")

library(RMark)

f.processed=process.data(df,model="Known")

f.ddl=make.design.data(f.processed)

run.fdata=function()


 Example model: S.time = list(formula=~time)
****Need to know how to format model for veg data over time***

 model.list=create.model.list("Known")
 f.results=mark.wrapper(model.list,data=f.processed,ddl=f.ddl,
 invisible=FALSE,threads=2)

 return(f.results)

f.results=run.fdata()
f.results

For my purpose, all fawns begin at the same day (i.e 1), but end at various days (based on whether they survived or not) up to the 70 day maximum. I know the [i] is incorrect, but I would like to test models like:

S.grass = list(formula=~g.[i])
S.forb = list(formula=~f.[i])
S.grass.plus.forb = list(formula=g.[i] + f.[i])

that will show how grass, forb, grass+forb, etc relate to survival. Maybe if an individual had more grass they were more likely to survive. Or perhaps an increase in forb meant a decrease in survival (things along this line of thinking).

I would appreciate any help or suggestions or even advice on where to go for help. I have already downloaded a couple Rmark manuals/help guides, yet I am still unable to figure it out.

Thank you for any help!
-Grad Student bashing their head on their monitor