Skip to content

Update alpha_diversity.py #79

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
recepcanaltinbag wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update alpha_diversity.py #79

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions DiversityTools/alpha_diversity.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,9 @@ def shannons_alpha(p):
for i in p:
h.append(i * math.log(i))
print("Shannon's diversity: %s" %(-1 *sum(h)))
# Comparison of different communities can be made if we normalize the Shannons by the maximum, It will take a
# value between 0 and 1. Evenness index = 1 means total evenness.
print("Normalized Shannon's diversity (Evenness index): %s" % ((-1 *sum(h)) / math.log((len(p)))))
return (-1 *sum(h))

def berger_parkers_alpha(p):
Expand Down