I think the calculation for initial EIR values isn't quite right. I d…

…on't think it needs to be multiplied by psi. When these values are drawn in lines 135-140 of biting_process.R they get multiplied by psi in line 144. That means we're effectively multiplying these values by psi^2. I think we can correct this by adjusting the calculation thusly.

The two tests at the end would then need adjusting (one way or another) to reflect this change - which could use improving.

R/biting_process.R

@@ -210,9 +210,7 @@ simulate_bites <- function(
 calculate_eir <- function(species, solvers, variables, parameters, timestep) {
   a <- human_blood_meal_rate(species, variables, parameters, timestep)
   infectious <- calculate_infectious(species, solvers, variables, parameters)
-  age <- get_age(variables$birth$get_values(), timestep)
-  psi <- unique_biting_rate(age, parameters)
-  infectious * a * mean(psi)
+  infectious * a
 }
 
 effective_biting_rates <- function(a, .pi, p_bitten) {

tests/testthat/test-biology.R

@@ -23,7 +23,10 @@ test_that('total_M and EIR functions are consistent with equilibrium EIR', {
   })
 
   expect_equal(
-    actual_EIR,
+    actual_EIR * 0.766,
+    # 0.766 is the population average psi under an exponential pop distribution
+    # There's possibly a better way of calculating this, depending on what exactly
+    # we're testing here, e.g., we could remove lines 19-21 and omega from line 22
     expected_EIR,
     tolerance = 1e-2
   )
@@ -51,7 +54,10 @@ test_that('total_M and EIR functions are consistent with equilibrium EIR (with h
   })
 
   expect_equal(
-    actual_EIR,
+    actual_EIR * 0.766,
+    # 0.766 is the population average psi under an exponential pop distribution
+    # There's possibly a better way of calculating this, depending on what exactly
+    # we're testing here, e.g., we could remove lines 49-51 and omega from line 52
     expected_EIR,
     tolerance = 1e-2
   )