tests and typo fix

.Rbuildignore

@@ -8,4 +8,5 @@
 ^PlottingScripts&
 R/ring-simulation7.R
 ^tools/
-PlottingScripts
+PlottingScripts
+News.md

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: hrp2malaRia
 Type: Package
 Title: pfhrp2 gene deletion malaria modelling
-Version: 0.1.1
-Date: 2019-03-20
+Version: 0.1.2
+Date: 2023-01-20
 Author: OJ Watson
 Maintainer: <[email protected]>
 Description: Individual based malaria transmission model.
@@ -13,9 +13,11 @@ Imports:
   reshape2,
   shiny
 Suggests:
-  context  
+    context,
+    testthat (>= 3.0.0)
 License: MIT + file LICENSE
 LazyData: TRUE
 RoxygenNote: 7.1.2
 Encoding: UTF-8
 Remotes: mrc-ide/context
+Config/testthat/edition: 3

R/NEWS.md → NEWS.md

@@ -1,3 +1,7 @@
+## hrp2malaRia 0.1.2
+
+* Fix to hrp2_Simulation introduced during previous version
+
 ## hrp2malaRia 0.1.1
 
 * microscopy 2-10 and PCR all ages now tracked in series

R/hrp2-simulation.R

@@ -1147,6 +1147,7 @@ hrp2_Simulation <- function(
 
       # Microscopy 2-10
       pos.2.10 <- which(res$Age<(365*10) & res$Age>(365*2))
+      total.2.10.over.time <- length(pos.2.10) * storage_capture
       pos.2.10_D.T <- arrayInd(which(res$Status[pos.2.10,last.7] %in% c(2,5)), dim(res$Status[pos.2.10,]))
       pos.2.10_A <- which(res$Status[pos.2.10,last.7] == 3, arr.ind = TRUE)
       pos.2.10_U <- which(res$Status[pos.2.10,last.7] == 4, arr.ind = TRUE)
@@ -1174,7 +1175,6 @@ hrp2_Simulation <- function(
 
       # PCR All age
       pos.allage_U <- which(res$Status[,last.7] == 4, arr.ind = TRUE)
-      total.2.10.over.time <- length(pos.2.10) * storage_capture
 
       # detectability of Us for PCR and microscopy all age
       f.D.U <- 1 - ((1 - f.D0) / (1 + ((res$Age[pos.allage_U[,1]] / a.D)^g.D)))

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/tests.html
+# * https://testthat.r-lib.org/reference/test_package.html#special-files
+
+library(testthat)
+library(hrp2malaRia)
+
+test_check("hrp2malaRia")

tests/testthat/test-runs.R

@@ -0,0 +1,12 @@
+test_that("sim runs", {
+  expect_output(
+  r <- hrp2malaRia::hrp2_Simulation(EIR = 1, N = 1000, years = 0.4)
+  )
+  expect_true("Buffer" %in% names(r))
+
+  expect_output(
+    r <- hrp2malaRia::hrp2_Simulation(EIR = 1, N = 1000, years = 0.4, 
+                                      just_storage_results = TRUE)
+  )
+  expect_false("Buffer" %in% names(r))
+})