[R] plotting survival curves (multiple curves on single graph)

[Bert Gunter]

Yes. Trellis plots are in the "lattice" package. My bad.

-- Bert

On Tue, Jul 5, 2011 at 3:22 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Quick note:
>
> On Tue, Jul 5, 2011 at 6:16 PM, Bert Gunter <gunter.berton at gene.com> wrote:
>> Yes, it can be done using basic plot commands.
>>
>> But if you really want to get fancy and plot "grouped" graphs, I
>> strongly recommend you look into R's packages -- ggplot or trellis.
>
> Attempting to clear out any confusion before it sets in: I'm pretty
> sure Bert meant "lattice" instead of "trellis".
>
> -steve
>
>> Both have excellent documentation and companion books and  were built
>> for this sort of thing. The (considerable) learning curve will be
>> worth the effort.
>>
>> Cheers,
>> Bert
>>
>> On Tue, Jul 5, 2011 at 3:08 PM, Trey Batey <ekt.batey at gmail.com> wrote:
>>> Hello.
>>>
>>> This is a follow-up to a question I posted last week.  With some
>>> previous suggestions from the R-help community, I have been able to
>>> plot survival (, hazard, and density) curves using published data for
>>> Siler hazard parameters from a number of ethnographic populations.
>>> Can the function below be modified, perhaps with a "for" statement, so
>>> that multiple curves (different line types---one for each population)
>>> are plotted on a single graph for comparison?  Thanks so much.
>>>
>>> --Trey
>>>
>>> The function and calls below use the data in this Excel file (feel
>>> free to access):
>>> https://docs.google.com/leaf?id=0B5zZGW2utJN0ZDk1NjA0ZjUtMWU0ZS00ZGQ3LWIxZTUtOWE0NGVmYWMxODJl&hl=en_US
>>>
>>> ## - plot Siler survival curve
>>> ##############################
>>> silsurv<-function(a1,b1,a2,a3,b3)
>>>  {
>>>    sil=function(t)
>>>      {
>>>        h.t<-a1*exp(-b1*t)+a2+a3*exp(b3*t)
>>>        S.t<-exp(-a1/b1*(1-exp(-b1*t))-a2*t+a3/b3*(1-exp(b3*t)))
>>>        d.t<-S.t*h.t
>>>
>>>        #return(d.t)
>>>        return(S.t)
>>>        #return(h.t)
>>>      }
>>>    t<-seq(0,90,1)
>>> plot(t,sil(t),ylim=c(0,1),type='l',cex.lab=0.8,cex.axis=0.75,ylab='S(t)',xlab='Age
>>> (years)')
>>>  }
>>>
>>> with(hazanth[1,3:7],silsurv(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3));title(main=hazanth[1,1],cex.main=0.9)
>>>  # plot for Hadza
>>> with(hazanth[2,3:7],silsurv(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3));title(main=hazanth[2,1],cex.main=0.9)
>>>  # plot for Ache
>>> with(hazanth[3,3:7],silsurv(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3));title(main=hazanth[3,1],cex.main=0.9)
>>>  # plot for Hiwi
>>> with(hazanth[4,3:7],silsurv(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3));title(main=hazanth[4,1],cex.main=0.9)
>>>  # plot for !Kung
>>> with(hazanth[5,3:7],silsurv(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3));title(main=hazanth[5,1],cex.main=0.9)
>>>  # plot for Yanomamo
>>> with(hazanth[6,3:7],silsurv(a1=a1,b1=b1,a2=a2,a3=a3,b3=b3));title(main=hazanth[6,1],cex.main=0.9)
>>>  # plot for Tsimane
>>>
>>> ###############################
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>>
>> --
>> "Men by nature long to get on to the ultimate truths, and will often
>> be impatient with elementary studies or fight shy of them. If it were
>> possible to reach the ultimate truths without the elementary studies
>> usually prefixed to them, these would not be preparatory studies but
>> superfluous diversions."
>>
>> -- Maimonides (1135-1204)
>>
>> Bert Gunter
>> Genentech Nonclinical Biostatistics
>> 467-7374
>> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
"Men by nature long to get on to the ultimate truths, and will often
be impatient with elementary studies or fight shy of them. If it were
possible to reach the ultimate truths without the elementary studies
usually prefixed to them, these would not be preparatory studies but
superfluous diversions."

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics
467-7374
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm