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

calc_ml uses no diversity dependence #43

Closed
Neves-P opened this issue Aug 3, 2020 · 2 comments
Closed

calc_ml uses no diversity dependence #43

Neves-P opened this issue Aug 3, 2020 · 2 comments
Assignees
@Neves-P
Labels
bug Something isn't working high priority To be done ASAP
Milestone
v1.0.3 release

Comments

@Neves-P
Copy link
Owner

Neves-P commented Aug 3, 2020

Most models in the studies using DAISIErobustness incorporate some form of diversity dependence. calc_ml() is calling DAISIE::DAISIE_ML_CS() with ddep = 0, i.e., no diversity dependence in the MLE. This should be changed to ddep = 11, meaning:

linear dependence in speciation rate and in immigration rate

Change calc_ml() and make appropriate corrections.
Further misspecifications of DD in the pipeline should also be checked for.
@Neves-P Neves-P added bug Something isn't working high priority To be done ASAP labels Aug 3, 2020
@Neves-P Neves-P added this to the v1.0.3 release milestone Aug 3, 2020
@Neves-P Neves-P self-assigned this Aug 3, 2020
Neves-P added a commit that referenced this issue Aug 3, 2020
@Neves-P
ddmodel = 11 for DD in MLE. Progress #43
bf1ce19
@Neves-P Neves-P mentioned this issue Aug 3, 2020
Open
@Neves-P
Copy link
Owner Author

Neves-P commented Aug 3, 2020

N.B.: All results obtain thus far must be checked as they're likely wrong unless DD is not considered from the start.

Neves-P added a commit that referenced this issue Aug 5, 2020
@Neves-P
Add utils file. Correct test-calc_ml references. Progress #43
5734162
Neves-P added a commit that referenced this issue Aug 5, 2020
@Neves-P
Correct test-run_analysis reference tests. Progress #43
83d02e9
Neves-P added a commit that referenced this issue Aug 5, 2020
@Neves-P
Fix test-run_robustness. Progress #43
8d59d5f
@Neves-P
Copy link
Owner Author

Neves-P commented Aug 5, 2020

Closed in 74d0dae

@Neves-P Neves-P closed this as completed Aug 5, 2020
@Neves-P Neves-P mentioned this issue Aug 5, 2020
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@Neves-P Neves-P

Labels
bug Something isn't working high priority To be done ASAP
Projects
None yet
Milestone
v1.0.3 release
Development

No branches or pull requests
1 participant
@Neves-P