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asfchallenge_ucd's Introduction

Repository for sharing code of the ASF Challange.

Some important dates:

Our weekly meeting time is Fridays 12 pm

  • First submission October 8 Results.
  • Second Submission November 23 RESULTS.
  • Third submission January 13. RESULTS.

Directory structure

|
|- Data: symlink with [Shared Box Folder](https://ucdavis.box.com/s/c3smpi8zby3qgg70scl5uyq1swl9kxag)  
|
|- Code: code for manuscript
|   |
|   |- R: for R, Rmd, and associated files
|   |
|   |- GAMA_ASF: for GAMA code (javascript syntax highlighting helps locally)
|
|- Figures: generated figures, maps, etc
|
|- Documentation: notes and results for sharing

Data:

The data original data and the data processed for the model can be found in the shared box folder. The Data provided is on the folders Data/Initialata and Data/Period_1. The processed data needed to run the model can be found on the folder Data/includes.

So many sick pigs !!!

Some Links:

Note

Parts of this code use the STNet package written by Pablo. To install it:

remotes::install_github("jpablo91/STNet")

#I am practicing, cause I need to

asfchallenge_ucd's People

Contributors

nistara avatar spablotemporal avatar jnbaronucd avatar kcohara avatar

Watchers

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asfchallenge_ucd's Issues

Implement the new interventions in GAMA

Implement the new interventions from the Day80.pdf file.
The challenge asks to estimate the effectiveness of 5 control options (they mention that if our model can not asses all of them, we can use only some):

  • Culling of all pig herds in protection zones (not in surveillance zones). Note that if a
    farm is in a protection zone when it has to be repopulated, the process is delayed until
    the protection zone is lifted.

  • Increasing the size of the active search area around infected wild boar carcasses found
    outside the fenced/buffer areas (from 1 km to 2 km)

  • Culling of all pig herds located at less than 3 km from positive wild boar carcasses

  • Increasing the size of the surveillance zone (from 10 km to 15 km, but still during 30
    days)

  • Culling of all herds that have traded pigs with an infected farm less than three weeks
    before detection

Update grid data for period 3

We need to use the new data provided to update the grid 1 new PH outbreaks and 997 WB carcasses have been detected since.

Revisit model used for period 1

Are there any things we can do better? some issues:

  • The model takes a while to setup every iteration because it reads a csv file and then runs a loop to get the neighbors for every agent, maybe we can find another approach for this.

  • The hunting pressure intervention uses a rate to decrease the population of WB, the challenge suggest to reduce the population in a 90%, we don't really account for this

Describe model parameters

Check the table of parameters and look for literature that can support our estimations used for the model

Update model for period 3

  • Update hunting pressure. hunting pressure will be implemented for other 10 days (until day 120)
  • Since day 90, depopulation of pig herds has been implemented in 3-km ratio around active cases (both wb and ph)

Check the pdf description for more info

Tasks for period 3

  • Update the predictions for effectiveness of fencing with and without hunting pressure

  • How likely is that the epidemic will fade in the next 4 months (230 days) given the new control measures

  • How likely is that there will be a second wave or become endemic on wild boars?

  • Suggestions to limit the risk

  • Can the control measures be lifted by the day 230?

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