Merge pull request #155 from mrc-ide/durations_together

v0.5.5 population$n as integer.
mrc-ide · Nov 25, 2020 · 8d0e69e · 8d0e69e
2 parents 9de967f + 1c55b96
commit 8d0e69e
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Showing 5 changed files with 16 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: squire
 Type: Package
 Title: SEIR transmission model of COVID-19
-Version: 0.5.4
+Version: 0.5.5
 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")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# squire 0.5.5
+
+* `population$n` are all integer class
+
 # squire 0.5.4
 
 * `beta_est` accepts apothecary models

diff --git a/data-raw/prepare_raw_data.R b/data-raw/prepare_raw_data.R
@@ -1,4 +1,5 @@
 # Process raw data
+library(tidyverse)
 
 # Contact Matrices sourced from literature used in the global report
 # ------------------------------------------------------------------------------
@@ -18,7 +19,7 @@ population <- demog %>%
   tidyr::pivot_longer(cols = -country, names_to = "age_group", values_to = "n",
                       names_prefix = "X") %>%
   dplyr::mutate(age_group = stringr::str_replace(age_group, "[.]", "-"),
-                n = round(n * 1000))
+                n = as.integer(round(n * 1000)))
 
 population$age_group <- factor(population$age_group, levels = c("0-4",
                                                                 "5-9",

diff --git a/data/population.rda b/data/population.rda
diff --git a/tests/testthat/test-population.R b/tests/testthat/test-population.R
@@ -102,3 +102,12 @@ test_that("durations", {
                     names(squire:::default_durations())))
 
 })
+
+
+
+test_that("population n are all integers", {
+
+  int_log <- vapply(population$n, is.integer, logical(1))
+  expect_true(sum(int_log) == length(population$n))
+
+})