[Basta-users] Making estimates precise

[Fernando Colchero]

Dear Cliff,

   Yes, in the Gompertz model both b0 and b1 are unbound, but in BaSTA b0 = log(a), where "a" is the scale parameter of the Gompertz model: mu(x) = a * exp(b1 * x). 

   I cc'ed the BaSTA mailing list in case someone has the same question.

    Best,

   Fernando

Fernando Colchero
Assistant Professor
Department of Mathematics and Computer Science
Max-Planck Odense Center on the Biodemography of Aging

Tlf.               +45 65 50 23 24
Email           colchero at imada.sdu.dk
Web             www.sdu.dk/staff/colchero
Pers. web   www.colchero.com
Adr.              Campusvej 55, 5230, Odense, Dk

University of Southern Denmark

On 1 Nov 2013, at 12:14, Cliff Cunningham <cliff at duke.edu> wrote:

> Dear Fernando,
> 
> 	Thanks again for your prompt reply.
> 
> 	Can I confirm that the bo parameter in the regular two parameter Gompertz can be negative as well as positive?  I know its the offset value, but in Adam's fitting model, he constrains bo to be positive.  BaSTA often gives negative values for bo, which is consistent with the absence of constraints indicated in your manual -infinity < b0 b1 > +infinity
> 
> 	But just wanted to make sure.
> 
> 	
> 	
> 	All the best!
> 
>    	Cliff Cunningham
> 
> 
>         Professor
> 	Biology Department
>     	Duke University
>         130 Science Drive
> 	Durham NC 27708
> 	Phone 919-660-7356
> 
> http://www.biology.duke.edu/cunningham
> 
> 
> 
> 
> On Nov 1, 2013, at 6:18 AM, Fernando Colchero wrote:
> 
>> Ah, ok. You can input continuous ages to the MakeLifeTable() function, but the output from the basta() function is integers. 
>> 
>>   Best,
>> 
>>   Fernando
>> 
>> Fernando Colchero
>> Assistant Professor
>> Department of Mathematics and Computer Science
>> Max-Planck Odense Center on the Biodemography of Aging
>> 
>> Tlf.               +45 65 50 23 24
>> Email           colchero at imada.sdu.dk
>> Web             www.sdu.dk/staff/colchero
>> Pers. web   www.colchero.com
>> Adr.              Campusvej 55, 5230, Odense, Dk
>> 
>> University of Southern Denmark
>> 
>> On 1 Nov 2013, at 11:10, Cliff Cunningham <cliff at duke.edu> wrote:
>> 
>>> Dear Fernando,
>>> Thanks again for your prompt reply.
>>> 
>>> If you go to ?? BaSTA, then Choose MakeLifeTable, the first vector is
>>> 
>>> DeathAges	
>>> A vector of ages at death. These can be precise (e.g. 5.4 yrs) or rounded to the integer year (e.g. 5 yrs).
>>> 
>>> 
>>> Package ‘BaSTA’
>>> This same text is in the 
>>> August 29, 2013 version of Package BaSTA (attached)
>>> 
>>> All the best!
>>> 
>>>    
>>> Cliff Cunningham
>>> 
>>> 
>>>         Professor
>>> Biology Department
>>>     
>>> Duke University
>>>         130 Science Drive
>>> Durham NC 27708
>>> Phone 919-660-7356
>>> 
>>> http://www.biology.duke.edu/cunningham
>>> 
>>> 
>>> 
>>> 
>>> On Nov 1, 2013, at 5:06 AM, Fernando Colchero wrote:
>>> 
>>>> Dear Cliff,
>>>> 
>>>>   I cannot find where in the documentation we say that agesQuant provides continuous age estimates, where did you find it so we can correct it? BaSTA right now works on unit time intervals and thus agesQuant provides the 50% quantile and the lower and upper 95% credible intervals for the age estimates. All three numbers are in time units, not continuous. We are working on extending BaSTA to take not only CMR data but other types of data as well, some of which will have continuous age. We'll have that in the future.
>>>> 
>>>>   Best,
>>>> 
>>>>    Fernando
>>>> 
>>>> Fernando Colchero
>>>> Assistant Professor
>>>> Department of Mathematics and Computer Science
>>>> Max-Planck Odense Center on the Biodemography of Aging
>>>> 
>>>> Tlf.               +45 65 50 23 24
>>>> Email           colchero at imada.sdu.dk
>>>> Web             www.sdu.dk/staff/colchero
>>>> Pers. web   www.colchero.com
>>>> Adr.              Campusvej 55, 5230, Odense, Dk
>>>> 
>>>> University of Southern Denmark
>>>> 
>>>> On 31 Oct 2013, at 15:11, Cliff Cunningham <cliff at duke.edu> wrote:
>>>> 
>>>>> Dear Fernando,
>>>>> 
>>>>> Thank you for the prompt reply.  Still, the documentation says that the agesQuant command can be delivered as real numbers instead of integers.  I assume this would be in the commands to create the basta object to begin with.  What command would that be?
>>>>> All the best!
>>>>> 
>>>>>    
>>>>> Cliff Cunningham
>>>>> 
>>>>> 
>>>>>         Professor
>>>>> Biology Department
>>>>>     
>>>>> Duke University
>>>>>         130 Science Drive
>>>>> Durham NC 27708
>>>>> Phone 919-660-7356
>>>>> 
>>>>> http://www.biology.duke.edu/cunningham
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Basta-users mailing list
>>>>> Basta-users at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/basta-users
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Fernando Colchero
>>>> Assistant Professor
>>>> Department of Mathematics and Computer Science
>>>> Max-Planck Odense Center on the Biodemography of Aging
>>>> 
>>>> Tlf.               +45 65 50 23 24
>>>> Email           colchero at imada.sdu.dk
>>>> Web             www.sdu.dk/staff/colchero
>>>> Pers. web   www.colchero.com
>>>> Adr.              Campusvej 55, 5230, Odense, Dk
>>>> 
>>>> University of Southern Denmark
>>>> 
>>> 
>>> <BaSTA.pdf>
>> 
> 

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