Skip to content
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

Jump to bottom

Pondering psex calculation #101

Closed
zkamvar opened this issue Apr 8, 2016 · 1 comment
Closed

Pondering psex calculation #101

zkamvar opened this issue Apr 8, 2016 · 1 comment
Labels
question
Milestone
poppr 2.4

Comments

@zkamvar
Copy link
Member

zkamvar commented Apr 8, 2016 •
edited
Loading

psex is currently calculated as

sum(dbinom(seq(n_samples_in_mlg), n_samples_in_mlg, pgen))

After looking at RClone, it's apparent that it's calculated as

dbinom(seq(n_samples_in_mlg) - 1, n_samples, pgen)

Which is basically saying that the probability of each ADDITIONAL clone being reproduced by sexual reproduction. I'm still not sure which is right, but it's clear that I need to take away that sum() and replace n_samples_in_mlg (second argument) with n_samples or n_mlg (or perhaps just G to let the user control it).
@zkamvar zkamvar modified the milestone: poppr 2.2 May 4, 2016
@zkamvar zkamvar modified the milestones: poppr 2.2, poppr 2.3 Jun 9, 2016
@zkamvar
Copy link
Member Author

zkamvar commented Mar 7, 2017

Stacy says to definitely remove that sum parameter and change it to the latter.

zkamvar added a commit that referenced this issue Mar 17, 2017
@zkamvar
add notes for #101 [skip ci]
fba769e
zkamvar added a commit that referenced this issue Mar 18, 2017
@zkamvar
something looks like it's working! [skip ci]
d15996e 
this is for #101
zkamvar added a commit that referenced this issue Mar 20, 2017
@zkamvar
set new method to default for #101
8132dc4
zkamvar added a commit that referenced this issue Mar 28, 2017
@zkamvar
add notes for #101 [skip ci]
ff9b042
zkamvar added a commit that referenced this issue Mar 28, 2017
@zkamvar
something looks like it's working! [skip ci]
6526c7c 
this is for #101
zkamvar added a commit that referenced this issue Mar 28, 2017
@zkamvar
set new method to default for #101
43d4553
zkamvar added a commit that referenced this issue Mar 29, 2017
@zkamvar
Add note about differences in formulation [skip ci]
e7fde08 
This further addresses #101. When adding tests for
the new implementation of psex, I found out that
the reduction presented in Parks and Werth was not
apparently the same. I'm not quite sure where to go
from here, but something's weird.
@zkamvar zkamvar mentioned this issue Apr 7, 2017
Merged
@zkamvar zkamvar closed this as completed Apr 8, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
question
Projects
None yet
Milestone
poppr 2.4
Development

No branches or pull requests
1 participant
@zkamvar