[R] question with drm function in "drc package"

[li li]

Thanks. I see what went wrong.


2015-12-07 16:33 GMT-05:00 Jeff Newmiller <jdnewmil at dcn.davis.ca.us>:

> The fine manual for the drm function mentions a parameter "logDose" ... I
> expect that since you did not specify it that the drm function is helpfully
> attempting to take the log of your data for you.
>
> I highly recommend reading up on making reproducible examples so your
> helpers can experiment with your problem directly instead of guessing by
> reading only. Of course, you would then want to post using plain text as
> the Posting Guide indicates so the HTML would not corrupt your code.
>
>
> http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
> --
> Sent from my phone. Please excuse my brevity.
>
> On December 7, 2015 1:05:32 PM PST, li li <hannah.hlx at gmail.com> wrote:
>>
>> Hi Jeff,
>>   I am not sure where the log of 0 was taken?
>>   Thanks.
>>     Li
>>
>> 2015-12-07 15:55 GMT-05:00 Jeff Newmiller <jdnewmil at dcn.davis.ca.us>:
>>
>>> Log of zero is infinity. Don't do that.
>>> --
>>> Sent from my phone. Please excuse my brevity.
>>>
>>> On December 7, 2015 12:15:48 PM PST, li li <hannah.hlx at gmail.com> wrote:
>>>
>>>> Hi all,
>>>>   I am trying to use the drm function in drc package to fit a 4 PL or 3PL
>>>> curve for an assay response. Please see the listed data below. When I do
>>>> the curve fitting, it returns the following error message. Anyone who
>>>> familiar with this have any input on what went wrong?
>>>>    Thanks so much in advance!!
>>>>       Hanna
>>>>
>>>>  dat
>>>>>
>>>>       values   log_dose
>>>> 1   -68.1125  3.9120230
>>>> 2   -73.8955  3.9120230
>>>> 3   -75.1235  3.9120230
>>>> 4   -47.3205  3.2188758
>>>> 5   -52.9835  3.2188758
>>>> 6   -58.0075  3.2188758
>>>> 7     8.2515  2.5257286
>>>> 8   -24.5925  2.5257286
>>>> 9   -18.1425  2.5257286
>>>> 10   75.3375  1.8325815
>>>> 11   89.3755  1.8325815
>>>> 12  115.9685  1.8325815
>>>> 13  345.7675  1.1394343
>>>> 14  470.8125
>>>> 1.1394343
>>>> 15  514.8985  1.1394343
>>>> 16
>>>> 1003.2235  0.4462871
>>>> 17 1033.0345  0.4462871
>>>> 18  866.1365  0.4462871
>>>> 19 1383.6525 -0.2468601
>>>> 20 1431.3245 -0.2468601
>>>> 21 1459.8025 -0.2468601
>>>> 22 1852.5795 -0.9400073
>>>> 23 1917.8015 -0.9400073
>>>> 24 1858.0875 -0.9400073
>>>> 25 1995.1185 -1.6331544
>>>> 26 2033.9455 -1.6331544
>>>> 27 1991.0405 -1.6331544
>>>> 28 2064.5855 -2.3263016
>>>> 29 2043.5195 -2.3263016
>>>> 30 2089.8525 -2.3263016
>>>> 31 2147.8445 -3.0194488
>>>> 32 2047.7905 -3.0194488
>>>> 33 2002.5375 -3.0194488
>>>> 34 2075.2665 -3.7125960
>>>> 35 2068.3545 -3.7125960
>>>> 36 2055.9605 -3.7125960
>>>>
>>>>>  mod1 <- drm(values~log_dose, fct=LL.4(), data=dat)
>>>>>
>>>> Error in optim(startVec, opfct, hessian = TRUE, method = optMethod, control
>>>> = list(maxit = maxIt,  :
>>>>   initial value in 'vmmin' is not
>>>> finite
>>>> Error in drmOpt(opfct, opdfct1, startVecSc,
>>>> optMethod, constrained,
>>>> warnVal,  :
>>>>   Convergence failed
>>>>
>>>>>
>>>>>
>>>>  [[alternative HTML version deleted]]
>>>>
>>>> ------------------------------
>>>>
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>>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>>
>>

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