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richardreeverichardreeve
authoredApr 19, 2021
Merge 37b7178 into 6aafff2 
2 parents 6aafff2 + 37b7178 commit 3987bbf

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‎.github/workflows/CompatHelper.yaml

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@@ -14,7 +14,7 @@ jobs:
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strategy:
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matrix:
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julia-version:
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- '1.6'
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- '1'
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arch:
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- x86
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os:
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with:
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version: ${{ matrix.julia-version }}
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arch: ${{ matrix.arch }}
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- name: Pkg.add("CompatHelper")
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- name: "Install CompatHelper"
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run: |
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julia -e '
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using Pkg
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Pkg.add("CompatHelper")'
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- name: CompatHelper.main()
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import Pkg
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name = "CompatHelper"
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uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
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version = "2"
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Pkg.add(; name, uuid, version)
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shell: julia --color=yes {0}
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- name: "Run CompatHelper"
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run: |
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import CompatHelper
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CompatHelper.main()
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shell: julia --color=yes {0}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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julia -e '
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using CompatHelper
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CompatHelper.main()'
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COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

‎.github/workflows/docs.yaml

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- name: Set up julia
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uses: julia-actions/setup-julia@v1
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with:
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version: '1.6'
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version: '1'
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arch: x64
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- name: Install dependencies
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run: |
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julia --project=docs/ -e '
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using Pkg
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Pkg.develop(PackageSpec(path=pwd()))
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import Pkg
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Pkg.develop(Pkg.PackageSpec(path=pwd()))
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Pkg.instantiate()
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Pkg.add("Documenter")'
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Pkg.add("Documenter")
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shell: julia --project=docs/ --color=yes {0}
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- name: Build and deploy
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run: |
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julia --project=docs/ --color=yes docs/make.jl

‎.github/workflows/testing.yaml

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pull_request:
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jobs:
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simulation-tests:
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EcoSISTEM-tests:
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runs-on: ${{ matrix.os }}
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continue-on-error: ${{ matrix.experimental }}
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strategy:

‎docs/src/simulation-jl.md

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**Table of datasets currently in use by EcoSISTEM.jl**
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# Datasets currently in use by EcoSISTEM.jl
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Preliminary list of parameters/datasets.
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| Name of parameter/ dataset | Description | Value | Source | Other info (e.g. stability) |
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| Name of parameter / dataset | Description | Value | Source | Other info (e.g. stability) |
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|----------------------------|-------------|-------|--------|-----------------------------|
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| p_s | Probability of developing symptoms | 0.96 | http://gabgoh.github.io/COVID/index.html (From Thibaud's original model) | |
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| p_h | Probability of hospitalisation | 0.2 | Guess | |
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| cfr_home | Case fatality ratio (at home) | 0.1 | Guess | |
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| cfr_hospital | Case fatality ratio (at hospital) | 0.1 | Guess | |
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| T_lat | Latent period | 5 days | http://gabgoh.github.io/COVID/index.html (From Thibaud's original model) | |
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| T_asym | Asymptomatic period | 3 days | http://gabgoh.github.io/COVID/index.html (From Thibaud's original model) | |
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| T_sym | Symptomatic period | 5 days | http://gabgoh.github.io/COVID/index.html (From Thibaud's original model) | |
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| T_hosp | Hospitalisation period | 5 days | https://www.icnarc.org/Our-Audit/Audits/Cmp/Reports (From Thibaud's original model) | |
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| T_rec | Recovery period | 11 days | http://gabgoh.github.io/COVID/index.html (From Thibaud's original model) | |
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| mu_1 | Probability of becoming Asymptomatic | 1/T_lat | | |
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| mu_2 | Probability of becoming Symptomatic | p_s * 1/T_asym | | |
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| hospitalisation | Probability of becoming Hospitalised | p_h * 1/T_sym | | |
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| sigma_1 | Probability of Recovery from Asymptomatic | (1 - p_s) * 1/T_asym | | |
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| sigma_2 | Probability of Recovery from Symptomatic | (1 - p_h) * (1 - cfr_home) * 1/T_rec | | |
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| sigma_hospital | Probability of Recovery from Hospital | (1 - cfr_hosp) * 1/T_hosp | | |
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| death_home | Probability of Death at home | cfr_home * 2/T_hosp | | |
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| death_hospital | Probability of Death at hospital | cfr_hosp * 1/T_hosp | | |
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| p_s | Probability of developing symptoms | 0.96 | [From Thibaud's original model](http://gabgoh.github.io/COVID/index.html) | |
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| p\_h | Probability of hospitalisation | 0.2 | Guess | |
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| cfr\_home | Case fatality ratio (at home) | 0.1 | Guess | |
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| cfr\_hospital | Case fatality ratio (at hospital) | 0.1 | Guess | |
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| T\_lat | Latent period | 5 days | [From Thibaud's original model](http://gabgoh.github.io/COVID/index.html) | |
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| T\_asym | Asymptomatic period | 3 days | [From Thibaud's original model](http://gabgoh.github.io/COVID/index.html) | |
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| T_sym | Symptomatic period | 5 days | [From Thibaud's original model](http://gabgoh.github.io/COVID/index.html) | |
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| T\_hosp | Hospitalisation period | 5 days | [From Thibaud's original model](https://www.icnarc.org/Our-Audit/Audits/Cmp/Reports) | |
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| T\_rec | Recovery period | 11 days | [From Thibaud's original model](http://gabgoh.github.io/COVID/index.html) | |
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| mu\_1 | Probability of becoming Asymptomatic | 1/T\_lat | | |
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| mu\_2 | Probability of becoming Symptomatic | p\_s \* 1/T\_asym | | |
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| hospitalisation | Probability of becoming Hospitalised | p\_h \* 1/T\_sym | | |
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| sigma\_1 | Probability of Recovery from Asymptomatic | (1 - p\_s) * 1/T\_asym | | |
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| sigma\_2 | Probability of Recovery from Symptomatic | (1 - p\_h) \* (1 - cfr\_home) * 1/T\_rec | | |
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| sigma_hospital | Probability of Recovery from Hospital | (1 - cfr_hosp) \* 1/T\_hosp | | |
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| death_home | Probability of Death at home | cfr\_home \* 2/T\_hosp | | |
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| death_hospital | Probability of Death at hospital | cfr\_hosp \* 1/T\_hosp | | |
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| ScotlandDensity2011 | Scottish population density at 1km grid | | UK census 2011 - A Reeves 'Covid19-ScottishCensusData' repo | |
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| dispersal_dist | Average dispersal distance of virus per disease category | 2.0km per infectious disease category | Guess | Varies depending on grid size |
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| mean_pref | Mean temperature preference of virus | 298K | Guess | Currently tuned to fit environment perfectly |
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| var_pref | Temperature niche width of virus | 0.1K | Guess | Currently tuned to fit environment perfectly |
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| dispersal\_dist | Average dispersal distance of virus per disease category | 2.0km per infectious disease category | Guess | Varies depending on grid size |
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| mean\_pref | Mean temperature preference of virus | 298K | Guess | Currently tuned to fit environment perfectly |
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| var\_pref | Temperature niche width of virus | 0.1K | Guess | Currently tuned to fit environment perfectly |
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| birth | Probability of giving birth per individual | 1.3e-4/day (20-40 year olds), 0 otherwise | Guess | |
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| death | Probability of giving natural mortality per individual | 2.7e-5/day | Guess | |
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| virus_growth_asymp | Rate of generating virus per asymptomatic individual | 0.1/day | Guess | |
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| virus_growth_symp | Rate of generating virus per symptomatic individual | 0.1/day | Guess | |
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| beta_force | Force of infection | 10.0/day | Guess | |
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| beta_env | Environmental transmission | 10.0/day | Guess | |
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| virus\_growth\_asymp | Rate of generating virus per asymptomatic individual | 0.1/day | Guess | |
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| virus\_growth\_symp | Rate of generating virus per symptomatic individual | 0.1/day | Guess | |
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| beta\_force | Force of infection | 10.0/day | Guess | |
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| beta\_env | Environmental transmission | 10.0/day | Guess | |

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