CARMA_fixed_sigma: incorrect description of the parameters

[Sodbo]

Dear CARMA team,

I am using the CARMA package for fine mapping (BTW - thanks for your work!).

I have faced a few problems with the description of CARMA_fixed_sigma_normal function, which prevents fine-tuning of the function for the purposes of large-scale analysis. I would appreciate if you would have a look at the comments below.

Many thanks!

Sodbo Sharapov

1. Line 16 : BF.index: A number smaller than 1 to specifying the threshold of the Bayes factor of the estimated credible models. The default setting is 3.2. 1.a: I assume it is not 3.2, but 1 / 3.2 1.b: Line 54 : In the function's code, the default value is: BF.index = 10. This is a contradiction. Can you please clarify and fix it, if needed?
2. Line 56 : The function's parameter outlier.BF.index = 1 / 3.2 (Line 56) lacks description, while parameter outlier.threshold (Line 18) does not exist in the code but is described in the description section. 2a. One may guess that outlier.BF.index and outlier.threshold are the same instances. Nevertheless, it could be clearer. 2b. Line 18 outlier.threshold | The Bayes threshold of the hypothesis testing of determining outliers, which is 10 by default.. But the default value is not concordant with the description and is outlier.BF.index = 1/3.2**.
3. Line 56 : The function's parameter tau = 0.04 lacks of description
4. Line 56: The function's parameter prior.prob.computation = "Logistic" lacks description.

[ZikunY]

Hi Sodbo,

Thank you for reaching out and pointing out the incorrect description. We will update the manual and description as soon as possible. Thanks again.

Best, Zikun