Shannon’s diversity index (SH)

[yuntwang]

Hi,
If my snp is bia-allelic, according to the formula: H=-ΣPilnPi
the range is 0-1.

Why is the value of this software so large, even greater than 1?

Hope to get the reply.
thanks.

[daveneti]

Thanks for your email, The range can be higher. Please give me some more details so I find out what the issue is. Guy

…

On Tue, 23 Feb 2021 at 10:35 PM, yuntwang ***@***.***> wrote: Hi, If my snp is bia-allelic, according to the formula: H=-ΣPilnPi the range is 0-1. Why is the value of this software so large, even greater than 1? Hope to get the reply. thanks. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#111>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAC32IPOJ5ETGTTM6GC4UB3TANZE5ANCNFSM4YCEKYSQ> .

[yuntwang]

Hi,&nbsp; In the paper <Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search&gt; Found a table:  SH is 4.531(4.399)，Why is it greater than 1？ According to the formula, I wrote a script myself, and the calculation result is between 0-1. When I use core-hunter to calculate, it is greater than 1. What I want to understand is why the SH in the paper is 4.531(4.399). Thanks.

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "corehunter/corehunter3" <[email protected]&gt;; 发送时间:&nbsp;2021年2月24日(星期三) 下午3:37 收件人:&nbsp;"corehunter/corehunter3"<[email protected]&gt;; 抄送:&nbsp;"wang"<[email protected]&gt;;"Author"<[email protected]&gt;; 主题:&nbsp;Re: [corehunter/corehunter3] Shannon’s diversity index (SH) (#111) Thanks for your email, The range can be higher. Please give me some more details so I find out what the issue is. Guy On Tue, 23 Feb 2021 at 10:35 PM, yuntwang <[email protected]&gt; wrote: &gt; Hi, &gt; If my snp is bia-allelic, according to the formula: H=-ΣPilnPi &gt; the range is 0-1. &gt; &gt; Why is the value of this software so large, even greater than 1? &gt; &gt; Hope to get the reply. &gt; thanks. &gt; &gt; — &gt; You are receiving this because you are subscribed to this thread. &gt; Reply to this email directly, view it on GitHub &gt; <#111&gt;, or unsubscribe &gt; <https://github.com/notifications/unsubscribe-auth/AAC32IPOJ5ETGTTM6GC4UB3TANZE5ANCNFSM4YCEKYSQ&gt; &gt; . &gt; — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[xiekunwhy]

Hi @daveneti ,

I also want to know why SH >1,
SH = -Σi Pi lnPi or SH = -Σi Pi logPi, where Pi is a proportion (frequencies, probabilities), there for values should be in interval 0 ≤ SH ≤ 1.

But it large than 1 in corehunter papers.

Best,
Kun

[hermandebeukelaer]

Hi @xiekunwhy,

I assume you are referring to one of the first two Core Hunter papers. In CH 1 and CH 2, Shannon's index was not scaled properly. A value between 0 and 1 was computed for each marker separately, based on the allele frequencies of that marker only. Those values were summed across all markers. Hence this could lead to a value (substantially) greater than 1.

In Core Hunter 3 the formula has been adjusted to calculate the formula globally across all markers, and should always yield a value between 0 and 1.

Does this answer your question, or did you come across a dataset for which Core Hunter 3 still yields SH values greater than 1?

Kind regards,
Herman