jidea-130 Replace Community Infections time series with Prevalence (#22)

* replace infect with prevalence

* lint

R/model_run.R

@@ -19,8 +19,12 @@ model_run <- function(parameters, model_version) {
     time_series,
     id_cols = "time", values_from = "value", names_from = "compartment"
   )
-  time_series$infect <- time_series$infect_asymp + time_series$infect_symp
-  time_series <- time_series[, c("infect",
+  time_series$prevalence <-
+    time_series$infect_asymp +
+    time_series$infect_symp +
+    time_series$hospitalised
+
+  time_series <- time_series[, c("prevalence",
                                 "hospitalised",
                                 "dead")]
 

inst/json/metadata_0.1.0.json

@@ -81,7 +81,10 @@
       }
     ],
     "time_series": [
-      { "id": "infect", "label": "Community infections", "description": "Infections not requiring hospitalisation" },
+      {
+        "id": "prevalence",
+        "label": "Prevalence",
+        "description": "Number of infectious individuals, comprising both symptomatic and asymptomatic infections, including those in need of hospitalisation." },
       { "id": "hospitalised", "label": "Hospital demand", "description": "Infections requiring hospitalisation" },
       { "id": "dead", "label": "Dead", "description": "Cumulative deaths" }
     ]

tests/testthat/test_model_run.R

@@ -43,10 +43,10 @@ test_that("can run model and return results", {
     "interventions",
     "capacities"
   ))
-  expect_named(res$time_series, c("infect",
+  expect_named(res$time_series, c("prevalence",
                                   "hospitalised",
                                   "dead"))
-  expect_identical(res$time_series$infect, c(16L, 56L))
+  expect_identical(res$time_series$prevalence, c(27L, 87L))
   expect_identical(res$time_series$hospitalised, c(11L, 31L))
   expect_identical(res$time_series$dead, c(15L, 35L))
   expect_identical(res$parameters, parameters)