Merge pull request #8 from mrc-ide/feat/eigen

.github/workflows/e2e.yml

@@ -21,16 +21,39 @@ jobs:
       - name: Install squire
         run: |
           R.exe -e "install.packages(c('V8', 'odin', 'deSolve', 'jsonlite', 'remotes'))"
-          R.exe -e "remotes::install_github(c('mrc-ide/odin.js', 'mrc-ide/squire'))"
+          R.exe -e "remotes::install_github(c('mrc-ide/odin.js', 'mrc-ide/squire@v0.4.8'))"
         shell: pwsh
       - name: Install Chrome
         run: |
-          $LocalTempDir = $env:TEMP; $ChromeInstaller = "ChromeInstaller.exe"; (new-object    System.Net.WebClient).DownloadFile('http://dl.google.com/chrome/install/375.126/chrome_installer.exe', "$LocalTempDir\$ChromeInstaller"); & "$LocalTempDir\$ChromeInstaller" /silent /install; $Process2Monitor =  "ChromeInstaller"; Do { $ProcessesFound = Get-Process | ?{$Process2Monitor -contains $_.Name} | Select-Object -ExpandProperty Name; If ($ProcessesFound) { "Still running: $($ProcessesFound -join ', ')" | Write-Host; Start-Sleep -Seconds 2 } else { rm "$LocalTempDir\$ChromeInstaller" -ErrorAction SilentlyContinue -Verbose } } Until (!$ProcessesFound)
+          $LocalTempDir = $env:TEMP
+          $ChromeInstaller = "ChromeInstaller.exe"
+          (new-object    System.Net.WebClient).DownloadFile('http://dl.google.com/chrome/install/375.126/chrome_installer.exe', "$LocalTempDir\$ChromeInstaller")
+          & "$LocalTempDir\$ChromeInstaller" /silent /install
+          $Process2Monitor =  "ChromeInstaller"
+          Do {
+            $ProcessesFound = Get-Process | ?{$Process2Monitor -contains $_.Name} | Select-Object -ExpandProperty Name
+            If ($ProcessesFound) {
+              "Still running: $($ProcessesFound -join ', ')" | Write-Host; Start-Sleep -Seconds 2
+            } else {
+              rm "$LocalTempDir\$ChromeInstaller" -ErrorAction SilentlyContinue -Verbose
+            }
+          } Until (!$ProcessesFound)
+        shell: pwsh
+      - name: Install Chromedriver
+        run: |
+          $chromeVersion = [System.Diagnostics.FileVersionInfo]::GetVersionInfo("C:\Program Files (x86)\Google\Chrome\Application\chrome.exe").FileVersion
+          $chromeDriverVersionPrefix = $chromeVersion.split(".")[0..2] -join "."
+          $chromeDriverVersionUrl = "https://chromedriver.storage.googleapis.com/LATEST_RELEASE_" + $chromeDriverVersionPrefix
+          $chromeDriverVersion = Invoke-RestMethod -Uri $chromeDriverVersionUrl
+          $chromeDriverZipLink = "https://chromedriver.storage.googleapis.com/" + $chromeDriverVersion + "/chromedriver_win32.zip"
+          Write-Output "Will download $chromeDriverZipLink"
+          $chromeDriverZipFileLocation = "chromedriver_win32.zip"
+          Invoke-WebRequest -Uri $chromeDriverZipLink -OutFile $chromeDriverZipFileLocation
+          Expand-Archive $chromeDriverZipFileLocation -Force
+          Remove-Item -Path $chromeDriverZipFileLocation -Force
         shell: pwsh
       - name: Test bundle
         run: |
-          curl --output chromedriver.zip https://chromedriver.storage.googleapis.com/81.0.4044.69/chromedriver_win32.zip
-          unzip chromedriver.zip
           npm install
           npm run build
           npm run e2e

.gitignore

@@ -1,3 +1,4 @@
 node_modules
 *.swp
 *.json
+.DS_Store

R/export.R

@@ -11,22 +11,26 @@ names(countries) <- unique(squire::population$iso3c)
 
 out_dir <- args[1]
 for (iso3c in names(countries)) {
+  R0 <- 3
   pars <- parameters_explicit_SEEIR(
     countries[[iso3c]],
     hosp_bed_capacity = 1, #dummy value
-    ICU_bed_capacity = 1  #dummy value
+    ICU_bed_capacity = 1,  #dummy value
+    R0 = R0
   )
 
   country_data <- list(
     population = pars$population,
     contactMatrix = pars$mix_mat_set,
-    beta = pars$beta
+    beta = pars$beta,
+    eigenvalue = R0 / pars$beta
   )
 
   write_json(
     country_data,
     file.path(out_dir, paste0(iso3c, '.json')),
     matrix='columnmajor',
+    auto_unbox=TRUE,
     digits=NA
   )
 }

README.md

@@ -91,3 +91,25 @@ Results will be an object representing a table of data. It will have the followi
 Names: The names of the columns of the table. The first name will be t, identifying the time step column. The following names will identify the state and the age group being counted in that column. The age group will be identified in square brackets. E.g. the "S[1]" column represents the count for susceptables in the first age group.
 
 Y: A 2D array representing the rows of the table. The first dimension will depend on the time steps and resolution of the model. The second dimension will be the same size as "Names".
+
+#### beta and Rt
+
+The model is parameterised with a country specific `beta` value.
+
+To translate Rt values into beta values, you can divide them by the country
+specific eigenvalue, e.g:
+
+```
+import nigeriaData from './data/NGA.json';
+const r0 = 3;
+const rt = [r0, r0/2];
+const beta = rt.map(r => { return r / nigeriaData.eigenvalue });
+```
+
+You can translate back to Rt by multiplying by the eigenvalue:
+
+```
+import nigeriaData from './data/NGA.json';
+const beta = [nigeriaData.beta, nigeriaData.beta/2];
+const rt = beta.map(r => { return r * nigeriaData.eigenvalue });
+```

test/test_index.js

@@ -56,6 +56,20 @@ describe('runModel', function() {
     })
   });
 
+  it('can translate between beta from R0', function() {
+    const beta = [stlucia.beta, stlucia.beta/2];
+    const r0 = 3;
+    const rt = [r0, r0/2];
+
+    rt.map(r => { return r / stlucia.eigenvalue }).forEach((value, i) => {
+      expect(beta[i]).to.be.closeTo(value, 1e-6);
+    });
+
+    beta.map(b => { return b * stlucia.eigenvalue }).forEach((value, i) => {
+      expect(rt[i]).to.be.closeTo(value, 1e-6);
+    });
+  });
+
   it('parameterises beds correctly', function() {
     const expected = pars;