Merge pull request #175 from mrc-ide/fix_parse_durations

parse_durations fix

Author: OJWatson

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: squire
 Type: Package
 Title: SEIR transmission model of COVID-19
-Version: 0.6.10
+Version: 0.6.11
 Authors@R: c(
   person("OJ", "Watson", email = "o.watson15@imperial.ac.uk", role = c("aut", "cre")),
   person("Patrick", "Walker", email = "patrick.walker06@imperial.ac.uk", role = c("aut")),

NEWS.md

@@ -1,3 +1,7 @@
+# squire 0.6.11
+
+* `parse_durations` bug fix. Handles dur_E, dur_IMild and dur_ICase correctly now
+
 # squire 0.6.10
 
 * `sample_pmcmc` bug fix dor negative posterior checks incorrectly. 

R/parameters.R

@@ -322,6 +322,9 @@ parameters_explicit_SEEIR <- function(
     dur_not_get_mv_die = dur_not_get_mv_die,
     dur_rec = dur_rec,
     dur_R = dur_R,
+    dur_E = dur_E,
+    dur_IMild = dur_IMild,
+    dur_ICase = dur_ICase,
     walker_params = walker_params)
 
   dur_get_ox_survive <- duration_params$dur_get_ox_survive

tests/testthat/test-run.R

@@ -281,3 +281,23 @@ test_that("default probs", {
                  "prob_severe_death_no_treatment","p_dist"))
 
 })
+
+
+
+test_that("duration E, IMild, ICase, changes through parse_durations", {
+
+  r <- run_deterministic_SEIR_model("Iran", time_period = 2, dur_E = 1, day_return = TRUE)
+  r2 <- run_deterministic_SEIR_model("Iran", time_period = 2, dur_E = 10, day_return = TRUE)
+  expect_true(r$parameters$gamma_E != r2$parameters$gamma_E)
+
+
+  r <- run_deterministic_SEIR_model("Iran", time_period = 2, dur_IMild = 1, day_return = TRUE)
+  r2 <- run_deterministic_SEIR_model("Iran", time_period = 2, dur_IMild = 10, day_return = TRUE)
+  expect_true(r$parameters$gamma_IMild != r2$parameters$gamma_IMild)
+
+
+  r <- run_deterministic_SEIR_model("Iran", time_period = 2, dur_ICase = 1, day_return = TRUE)
+  r2 <- run_deterministic_SEIR_model("Iran", time_period = 2, dur_ICase = 10, day_return = TRUE)
+  expect_true(r$parameters$gamma_ICase != r2$parameters$gamma_ICase)
+
+})