Merge pull request #22 from dd-harp/dev

xde_scaling_eir
dd-harp · Oct 14, 2024 · 7096f1d · 7096f1d
2 parents a2a9fcf + 802feb7
commit 7096f1d
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Showing 41 changed files with 2,246 additions and 1,941 deletions.
diff --git a/.gitignore b/.gitignore
@@ -11,3 +11,5 @@ docs/*.html
 /docs
 docs/reference/ar_compare.html
 *.html
+/docs/articles
+/docs
diff --git a/R/scaling.R b/R/scaling.R
@@ -17,11 +17,10 @@ xde_scaling_eir = function(model, N=25){
   for(i in 1:N){
     model$EIRpar$eir <- aEIR[i]/365
     model <- ramp.xds::xds_solve_cohort(model, A=10, da=1)
-    XH <- model$outputs$orbits$XH[[1]]
-    terms <- model$outputs$orbits$terms[[1]]
+    XH <- get_XH(model, 1)
     pr_t = tail(XH$true_pr, 365); pr[i] = mean(pr_t)
     ni_t = tail(XH$ni, 365);  ni[i]= mean(ni_t)
-    eir_t = tail(terms$EIR, 365); eir[i] = mean(eir_t)
+    eir_t = tail(XH$eir, 365); eir[i] = mean(eir_t)
     scaling[[i]] = list(aeir = eir_t*365, eir = eir_t, pr = pr_t, ni = ni_t)
   }
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -62,3 +62,8 @@ reference:
   - xde_scaling_Z
   - xde_scaling_eir
   - xde_scaling_lambda
+- title: Demography
+  desc: |
+    No methods to set subclass
+  contents:
+  - UnevenAgingMatrix
diff --git a/docs/articles/Analysis.html b/docs/articles/Analysis.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,3 +11,5 @@ docs/*.html @@
     /docs
     docs/reference/ar_compare.html
     *.html
+    /docs/articles
+    /docs