[R] integrate function - error -integration not occurring with last few rows

[Peter Ehlers]

On 2012-04-06 07:19, Navin Goyal wrote:
> Thank you so much for your help Berend.
> I did not see that my code had a typo and it was thus wrongly written ( I
> overlooked the i that was supposed to be actually 1)
>
> instead of       for (q in *1*:length(comb1$ID))
>   I had it as         for (q in *i*:length(comb1$ID))

This is a good example to show that it's usually better to
use seq_along() or seq_len() instead of 1:x.

Peter Ehlers

>
> It works correctly as expected
> Thanks again.
>
>
> Navin
>
>
>
>
>
>
> On Fri, Apr 6, 2012 at 9:56 AM, Berend Hasselman<bhh at xs4all.nl>  wrote:
>
>>
>> On 06-04-2012, at 13:14, Navin Goyal wrote:
>>
>>> Apologies for the lengthy code.
>>> I tried a simple (and shorter) piece of code (pasted below) and it still
>> gives me the same error for last few rows. Is this a bug or am I doing
>> something totally wrong?  Could anyone please provide some help/pointers ?
>>>
>>
>> You are not specifying what the  error is for the last few rows?
>> You are doing something completely wrong (AFAICT).
>> See below.
>>
>>> PS.  beta0 was fixed to 0.001 in the previous code. Also if I manually
>> estimated the integral isnt 0. If I scramble the row order, it is again
>> only the last few rows that dont integrate.
>>
>> See below.
>>
>>> Thanks
>>>
>>> data1<-expand.grid(1:5,0:6,10)
>>> names(data1)<-c("ID","TIME", "DOSE")
>>> data1<-data1[order(data1$DOSE,data1$ID,data1$TIME),]
>>> ed<-data1[!duplicated(data1$ID) , c(1,3)]
>>> ed$base=1
>>> ed$drop=1
>>> set.seed(5234123)
>>> k<-0
>>> for (i in 1:length(ed$ID))
>>> {
>>> k<-k+1
>>> ed$base[k]<-100*exp(rnorm(1,0,0.2))
>>> ed$drop[k]<-0.20*exp(rnorm(1,0,0.5))
>>> }
>>
>> Why are you not using i to index ed$XXX?
>> You are not using i.
>> Simplify to
>>
>> for (k in 1:length(ed$ID))
>> {
>> ed$base[k]<-100*exp(rnorm(1,0,0.2))
>> ed$drop[k]<-0.20*exp(rnorm(1,0,0.5))
>> }
>>
>>> comb1<-merge(data1[, c("ID","TIME")], ed)
>>> comb1$disprog<-comb1$base*exp(-comb1$drop*comb1$TIME)
>>> comb1$integral=0
>>> hz.func1<-function(t,bshz,beta1, change)
>>> { ifelse(t==0,bshz, bshz*exp(beta1*change)) }
>>
>> Insert here
>>
>> comb1
>> i
>> length(comb1$ID)
>>
>> and you should see that i is 5 and that length(comb1$ID) is 35.
>>
>>> q<-0
>>> for (m in i:length(comb1$ID))
>>> {
>>> q<-q+1
>>> comb1$integral[q]<-integrate(hz.func1, lower=0, upper=comb1$TIME[q],
>>>            bshz=0.001,beta1=0.035,
>>>           change=comb1$disprog[q])$value
>>> }
>>> comb1
>>>
>>
>> 1. Why does your for loop variable m start with i and not 1? (as I told
>> you in my first reply)
>> 2. Why are you not using the for loop variable m?
>> 3. So from the above m starts at 5 and stops at 35 (==>  312 steps)
>> 4, so you are filling elements 1 to 31 of comb1 and items 32 to 35 are
>> unchanged.
>>
>> 5. why don't you do this
>>
>> for (q in 1:length(comb1$ID))
>> {
>> comb1$integral[q]<-integrate(hz.func1, lower=0, upper=comb1$TIME[q],
>>           bshz=0.001,beta1=0.035,
>>          change=comb1$disprog[q])$value
>> }
>> comb1
>>
>> This avoids a useless variable m and fill all elements of comb1.
>> And you could just as well reuse variable k; there is no need for a new
>> variable (q) here.
>>
>> Berend
>>
>>
>>
>
>