All, I am struggling to create a survival plot using LTRC data for each year of a 10 year period. I have a set of individuals (birds) where 'entry' is the day of the year (1-365) they are released (let out of pens) into the wild (2 year data snip below). 'Entry' (e.g., day of year the first bird is released for each year) is highly variable, ranging from 48 to >250. When I create a plot using the below code I would like to remove the 'solid' line which represent S_hat=1 out to the LC point for each year and instead have the survival curves formatted in more of a 'hanging' style, where the LC day (e.g., min(Entry for each year)) is where each curve begins at S_hat=1 for each year (and does not extend back to the y-axis)? I could not find anything on this in the archives or MASS or Survival Analysis using S? Anyone have a suggestion on where to look? TIA, Bret #Code snip for R email. apc.coxfit1<-coxph(Surv(Entry, Exit, Fate)~Sex + Agerelease + Dayrelease + strata(Year), data=mydat) coxfit.apc<-survfit(apc.coxfit1) coxfit.apc plot(survfit(apc.coxfit1), conf.int=F, log=T, lty=c(1:2), col=c(1:2), xlim=c(205, 800)) #not run--first entry for this example is day 205 for 1996, 259 for 1997>mydatID Year Dayrelease Agerelease Survivorship Entry Exit Fate Sex 16240 1996 205 95 164 205 369 1 0 16319 1996 205 88 140 205 345 1 0 16378 1996 248 108 100 248 348 1 0 20383 1996 241 98 204 241 445 1 0 16324 1996 219 90 227 219 446 1 0 16327 1996 219 90 497 219 716 1 0 20373 1996 241 114 413 241 654 1 0 20374 1996 241 111 211 241 452 1 0 16241 1996 205 95 234 205 439 1 1 16321 1996 219 90 118 219 337 1 1 16323 1996 219 90 180 219 399 1 1 20375 1996 241 103 268 241 509 1 1 20384 1996 241 98 299 241 540 1 1 20390 1996 241 93 204 241 445 1 1 20393 1996 241 88 208 241 449 1 1 16313 1996 248 122 512 248 760 0 1 20378 1996 241 103 236 241 477 0 1 20381 1996 241 101 329 241 570 0 1 16328 1996 219 90 224 219 443 0 1 16827 1997 259 127 52 259 311 1 0 16828 1997 259 127 216 259 475 1 0 16831 1997 303 171 19 303 322 1 0 20466 1997 289 149 31 289 320 1 0 20469 1997 289 149 199 289 488 1 0 20483 1997 289 134 18 289 307 1 0 16807 1997 259 137 223 259 482 1 0 16809 1997 259 137 1 259 260 1 0 16819 1997 259 131 237 259 496 1 0 16829 1997 303 171 7 303 310 1 0 20440 1997 289 161 7 289 296 1 0 20470 1997 289 148 257 289 546 1 0 20478 1997 289 143 12 289 301 1 0 16817 1997 259 130 85 259 344 1 0 20454 1997 289 154 4 289 293 1 1 20459 1997 289 153 335 289 624 1 1 20460 1997 289 153 118 289 407 1 1 20465 1997 289 150 31 289 320 1 1 20473 1997 289 147 65 289 354 1 1 20484 1997 289 133 58 289 347 1 1 20489 1997 289 130 56 289 345 1 1 16808 1997 259 137 137 259 396 0 1 16810 1997 303 181 64 303 367 0 1 16816 1997 259 130 1 259 260 0 1 20471 1997 289 147 334 289 623 0 1 16826 1997 259 127 20 259 279 0 1
I don't see any easy way to do this. I think you may have to do the
plotting yourself, based on the code in plot.survfit.
-thomas
On Wed, 8 Mar 2006, Bret Collier wrote:
> All,
> I am struggling to create a survival plot using LTRC data for each year
> of a 10 year period.
>
> I have a set of individuals (birds) where 'entry' is the day of the
> year (1-365) they are released (let out of pens) into the wild (2 year
> data snip below). 'Entry' (e.g., day of year the first bird is
> released for each year) is highly variable, ranging from 48 to >250.
> When I create a plot using the below code I would like to remove the
> 'solid' line which represent S_hat=1 out to the LC point for each
year
> and instead have the survival curves formatted in more of a
'hanging'
> style, where the LC day (e.g., min(Entry for each year)) is where each
> curve begins at S_hat=1 for each year (and does not extend back to the
> y-axis)? I could not find anything on this in the archives or MASS or
> Survival Analysis using S? Anyone have a suggestion on where to look?
>
> TIA, Bret
>
>
> #Code snip for R email.
> apc.coxfit1<-coxph(Surv(Entry, Exit, Fate)~Sex + Agerelease +
> Dayrelease + strata(Year), data=mydat)
> coxfit.apc<-survfit(apc.coxfit1)
> coxfit.apc
> plot(survfit(apc.coxfit1), conf.int=F, log=T, lty=c(1:2), col=c(1:2),
> xlim=c(205, 800)) #not run--first entry for this example is day 205 for
> 1996, 259 for 1997
>
>> mydat
> ID Year Dayrelease
> Agerelease Survivorship Entry Exit Fate Sex
> 16240 1996 205 95 164 205 369 1 0
> 16319 1996 205 88 140 205 345 1 0
> 16378 1996 248 108 100 248 348 1 0
> 20383 1996 241 98 204 241 445 1 0
> 16324 1996 219 90 227 219 446 1 0
> 16327 1996 219 90 497 219 716 1 0
> 20373 1996 241 114 413 241 654 1 0
> 20374 1996 241 111 211 241 452 1 0
> 16241 1996 205 95 234 205 439 1 1
> 16321 1996 219 90 118 219 337 1 1
> 16323 1996 219 90 180 219 399 1 1
> 20375 1996 241 103 268 241 509 1 1
> 20384 1996 241 98 299 241 540 1 1
> 20390 1996 241 93 204 241 445 1 1
> 20393 1996 241 88 208 241 449 1 1
> 16313 1996 248 122 512 248 760 0 1
> 20378 1996 241 103 236 241 477 0 1
> 20381 1996 241 101 329 241 570 0 1
> 16328 1996 219 90 224 219 443 0 1
> 16827 1997 259 127 52 259 311 1 0
> 16828 1997 259 127 216 259 475 1 0
> 16831 1997 303 171 19 303 322 1 0
> 20466 1997 289 149 31 289 320 1 0
> 20469 1997 289 149 199 289 488 1 0
> 20483 1997 289 134 18 289 307 1 0
> 16807 1997 259 137 223 259 482 1 0
> 16809 1997 259 137 1 259 260 1 0
> 16819 1997 259 131 237 259 496 1 0
> 16829 1997 303 171 7 303 310 1 0
> 20440 1997 289 161 7 289 296 1 0
> 20470 1997 289 148 257 289 546 1 0
> 20478 1997 289 143 12 289 301 1 0
> 16817 1997 259 130 85 259 344 1 0
> 20454 1997 289 154 4 289 293 1 1
> 20459 1997 289 153 335 289 624 1 1
> 20460 1997 289 153 118 289 407 1 1
> 20465 1997 289 150 31 289 320 1 1
> 20473 1997 289 147 65 289 354 1 1
> 20484 1997 289 133 58 289 347 1 1
> 20489 1997 289 130 56 289 345 1 1
> 16808 1997 259 137 137 259 396 0 1
> 16810 1997 303 181 64 303 367 0 1
> 16816 1997 259 130 1 259 260 0 1
> 20471 1997 289 147 334 289 623 0 1
> 16826 1997 259 127 20 259 279 0 1
>
> ______________________________________________
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Thomas Lumley Assoc. Professor, Biostatistics
tlumley at u.washington.edu University of Washington, Seattle
Thomas, Thank you for the response. I will post what I come up with. Bret>>> Thomas Lumley <tlumley at u.washington.edu> 03/08/06 9:16 AM >>>I don't see any easy way to do this. I think you may have to do the plotting yourself, based on the code in plot.survfit. -thomas On Wed, 8 Mar 2006, Bret Collier wrote:> All, > I am struggling to create a survival plot using LTRC data for eachyear> of a 10 year period. > > I have a set of individuals (birds) where 'entry' is the day of the > year (1-365) they are released (let out of pens) into the wild (2year> data snip below). 'Entry' (e.g., day of year the first bird is > released for each year) is highly variable, ranging from 48 to >250. > When I create a plot using the below code I would like to remove the > 'solid' line which represent S_hat=1 out to the LC point for eachyear> and instead have the survival curves formatted in more of a'hanging'> style, where the LC day (e.g., min(Entry for each year)) is whereeach> curve begins at S_hat=1 for each year (and does not extend back tothe> y-axis)? I could not find anything on this in the archives or MASSor> Survival Analysis using S? Anyone have a suggestion on where tolook?> > TIA, Bret > > > #Code snip for R email. > apc.coxfit1<-coxph(Surv(Entry, Exit, Fate)~Sex + Agerelease + > Dayrelease + strata(Year), data=mydat) > coxfit.apc<-survfit(apc.coxfit1) > coxfit.apc > plot(survfit(apc.coxfit1), conf.int=F, log=T, lty=c(1:2),col=c(1:2),> xlim=c(205, 800)) #not run--first entry for this example is day 205for> 1996, 259 for 1997 > >> mydat > ID Year Dayrelease > Agerelease Survivorship Entry Exit Fate Sex >16240 1996 205 95 164 205 369 1 0>16319 1996 205 88 140 205 345 1 0>16378 1996 248 108 100 248 348 1 0>20383 1996 241 98 204 241 445 1 0>16324 1996 219 90 227 219 446 1 0>16327 1996 219 90 497 219 716 1 0>20373 1996 241 114 413 241 654 1 0>20374 1996 241 111 211 241 452 1 0>16241 1996 205 95 234 205 439 1 1>16321 1996 219 90 118 219 337 1 1>16323 1996 219 90 180 219 399 1 1>20375 1996 241 103 268 241 509 1 1>20384 1996 241 98 299 241 540 1 1>20390 1996 241 93 204 241 445 1 1>20393 1996 241 88 208 241 449 1 1>16313 1996 248 122 512 248 760 0 1>20378 1996 241 103 236 241 477 0 1>20381 1996 241 101 329 241 570 0 1>16328 1996 219 90 224 219 443 0 1>16827 1997 259 127 52 259 311 1 0>16828 1997 259 127 216 259 475 1 0>16831 1997 303 171 19 303 322 1 0>20466 1997 289 149 31 289 320 1 0>20469 1997 289 149 199 289 488 1 0>20483 1997 289 134 18 289 307 1 0>16807 1997 259 137 223 259 482 1 0>16809 1997 259 137 1 259 260 1 0>16819 1997 259 131 237 259 496 1 0>16829 1997 303 171 7 303 310 1 0>20440 1997 289 161 7 289 296 1 0>20470 1997 289 148 257 289 546 1 0>20478 1997 289 143 12 289 301 1 0>16817 1997 259 130 85 259 344 1 0>20454 1997 289 154 4 289 293 1 1>20459 1997 289 153 335 289 624 1 1>20460 1997 289 153 118 289 407 1 1>20465 1997 289 150 31 289 320 1 1>20473 1997 289 147 65 289 354 1 1>20484 1997 289 133 58 289 347 1 1>20489 1997 289 130 56 289 345 1 1>16808 1997 259 137 137 259 396 0 1>16810 1997 303 181 64 303 367 0 1>16816 1997 259 130 1 259 260 0 1>20471 1997 289 147 334 289 623 0 1>16826 1997 259 127 20 259 279 0 1> > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide!http://www.R-project.org/posting-guide.html>Thomas Lumley Assoc. Professor, Biostatistics tlumley at u.washington.edu University of Washington, Seattle