anyadoc/OvCWDWkshp.md

## OvCWDWkshp.md

      
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              OvCWDWkshp.md
            
          
9th April 2024, 9 a.m. to 12 p.m.

OvCWD Modeling Framework: Applications for CWD Management and Research

9th April 2024, 2 p.m. to 5 p.m.

Adapting OvCWD Models for regional white-tailed deer populations


Department of Veterinary and Biomedical Sciences, University of Minnesota, College of Veterinary Medicine, 1971 Commonwealth Avenue, St. Paul, Minnesota 55108


Funding for Workshops provided by the Safari Club International Foundation


Right-click on the links and open in a new tab.

1. Download NetLogo (Version 6.3.0)

https://ccl.northwestern.edu/netlogo/download.shtml
For more info: https://ccl.northwestern.edu/netlogo/index.shtml

2. Download Notepad++

https://notepad-plus-plus.org/downloads/v8.5.6/

3. Download OvCWD Models

a) INOvPOP: https://doi.org/10.25937/qy95-2d14
Click on the green Download button in the upper right corner.
Extract all and save all the folders on your computer in a new folder titled 'OvPOP'.
b) INOvCWD: https://doi.org/10.25937/wx4k-wv30
Click on the green Download button in the upper right corner.
Extract all and save all the folders on your computer in a new folder titled 'OvCWD'.

4. Understanding directory structure for model codebase


1) Attention to details: Setting up model scenarios

2) Saving output files: avoid overwriting!

3) Snapshot of model interface for reference: Export Interface, save as .png


5. Model Calibration: Generating a realistic deer population with INOvPOP

1) Data request form: https://github.com/anyadoc/OvCWDWorkshop/blob/main/Data%20for%20OvCWD.pdf

2a) Group 1: Select LaPorte from the drop dowen menu ('region') and set INOvPOP interface sliders as seen in 4.3 above.

2b) Group 2: Select LaPorte from the drop dowen menu ('region') and set INOvPOP interface sliders as follows:

i) post_harvest_density 37 per sq. mile
ii) sexratio 120
iii) adultprop 0.40
3) Iterative analysis

Use BehaviorSpace to run 10 iterations for each group.
4) Automated model output analysis using ShinyOvCWD

a) Submit the request for access to ShinyOvCWD: https://github.com/anyadoc/OvCWDWorkshop/blob/main/Access%20Request%20Form%20for%20OvCWD%20Analysis%20Shiny%20App.pdf
b) Set sliders (Instructions tab) as follows and upload the two files saLaPorte.csv and deerpopdyLaPorte from the 'results' folder; then check the plots & tables by clicking on the tabs 'OvPOP: Preharvest population' and 'OvPOP: Population structure & harvest'.

c) Compare outputs for the two groups


6. Simulating CWD spread in LaPorte deer population with INOvCWD

a) Import LaPorte County deer population snapshot into INOvCWD: Copy 'PostHarvestPopulationLaPorte_v2.2.0.csv' from the INOvPOP results folder and paste it in INOvCWD 'data' folder.
b) Right click on the 'cwd_region' button, click on 'Edit...', type "LaPorte" in the box and click 'OK'.

c) Click on the 'code' tab, go to line 174, press enter and type the following line:
if (cwd_region = "LaPorte") [ import-world "../data/PostHarvestPopulationLaPorte_v2.2.0.csv" ]
If you dont see line numbers, click on 'Tools' -> 'Preferences' -> Select 'Show Line Numbers (in editor)' -> 'OK'.
d) Click 'File' -> 'Save'. Click 'Interface' -> Setup -> Wait until setup is completed and then click Go.
e) Interpreting OvCWD outputs
Persistent CWD outbreak

Fadeout

f) Run 100 iterations using BehaviorSpace.
g) Automated model output analysis using ShinyOvCWD. Upload output file cwdinfdyLaPorte_seedinf_1.csv from the results folder as shown below. This file is available to download here (click on the link -> right click -> Save as .csv): https://raw.githubusercontent.com/anyadoc/OvCWDWorkshop/main/cwdinfdyLaPorte_seedinf_1_bl.csv
Click on 'OvCWDDy: CWD trajectories' to explore model outputs.


7. OvCWD outputs: Interpretation and Application

a) Demographic competence: Ability of a host population to sustain an infectious disease outbreak (Silk, M.J., Hodgson, D.J. Life history and population regulation shape demographic competence and influence the maintenance of endemic disease. Nat Ecol Evol 5, 82–91 (2021). https://doi.org/10.1038/s41559-020-01333-8)

Assessing the risk of establishment in regional deer populations: Montcalm County MI

Virtual experimentation: What if scenarios - APR implemented in Montcalm County MI

b) CWD trajectory
Nuanced scenarios - incorporate real-world processess

CWD prevalence trajectory

c) Outbreak probabilities


d) Force of infection
FOI is defined as the per capita rate at which susceptible individuals in a population get infected per unit time (Emilia and White, 2010).
FOI facilitates the estimation of disease burdens, and the impact of disease management interventions in particular  (Hens et al., 2010).
As OvCWDDy is an agent-based model, the actual number of successful transmissions occurring during a given time step can be readily documented to calculate FOI. Any changes in FOI reflect changes in the per capita risk of CWD infection.FOI is a standalone metric to effectively quantify changes in CWD transmission and compare efficacy of alternate management interventions.

e) Phase-specific strategies


8. Developing tools for meaningful stakeholder engagement


APR Dashboard
APR Shiny App


8. Bookmark Shiny Apps / Shiny Dashboards


getascii: https://anyadoc.shinyapps.io/getascii/


shinyOvCWD: https://anyadoc.shinyapps.io/shinyOvCWD/


Rate2Probability: https://anyadoc.shinyapps.io/Rate2Prob/


APR strategies: https://anyadoc.shinyapps.io/DeerHarvestCWD1/


APR Dashboard: https://rpubs.com/anyadoc/OvCWD_APR


CWD in USA (work in progress): https://anyadoc.shinyapps.io/CWDinUSA/


Aniruddha Belsare, PhD 

Assistant Professor of Disease Ecology 

Email: abelsare@auburn.edu
Website: https://avbelsare.netlify.app
Twitter: https://twitter.com/anyadoc