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Merge 37b7178 into 6aafff2
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@richardreeve
richardreeve authored Apr 19, 2021
2 parents 6aafff2 + 37b7178 commit 3987bbf
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24 changes: 14 additions & 10 deletions .github/workflows/CompatHelper.yaml
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Expand Up @@ -14,7 +14,7 @@ jobs:
strategy:
matrix:
julia-version:
- '1.6'
- '1'
arch:
- x86
os:
Expand All @@ -24,15 +24,19 @@ jobs:
with:
version: ${{ matrix.julia-version }}
arch: ${{ matrix.arch }}
- name: Pkg.add("CompatHelper")
- name: "Install CompatHelper"
run: |
julia -e '
using Pkg
Pkg.add("CompatHelper")'
- name: CompatHelper.main()
import Pkg
name = "CompatHelper"
uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
version = "2"
Pkg.add(; name, uuid, version)
shell: julia --color=yes {0}
- name: "Run CompatHelper"
run: |
import CompatHelper
CompatHelper.main()
shell: julia --color=yes {0}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
julia -e '
using CompatHelper
CompatHelper.main()'
COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
10 changes: 5 additions & 5 deletions .github/workflows/docs.yaml
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Expand Up @@ -18,15 +18,15 @@ jobs:
- name: Set up julia
uses: julia-actions/setup-julia@v1
with:
version: '1.6'
version: '1'
arch: x64
- name: Install dependencies
run: |
julia --project=docs/ -e '
using Pkg
Pkg.develop(PackageSpec(path=pwd()))
import Pkg
Pkg.develop(Pkg.PackageSpec(path=pwd()))
Pkg.instantiate()
Pkg.add("Documenter")'
Pkg.add("Documenter")
shell: julia --project=docs/ --color=yes {0}
- name: Build and deploy
run: |
julia --project=docs/ --color=yes docs/make.jl
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2 changes: 1 addition & 1 deletion .github/workflows/testing.yaml
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Expand Up @@ -10,7 +10,7 @@ on:
pull_request:

jobs:
simulation-tests:
EcoSISTEM-tests:
runs-on: ${{ matrix.os }}
continue-on-error: ${{ matrix.experimental }}
strategy:
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52 changes: 26 additions & 26 deletions docs/src/simulation-jl.md
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@@ -1,33 +1,33 @@
**Table of datasets currently in use by EcoSISTEM.jl**
# Datasets currently in use by EcoSISTEM.jl

Preliminary list of parameters/datasets.

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

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