Add tests

tests/testthat/_snaps/epichains.md

@@ -0,0 +1,218 @@
+# print.epichains works for simulation functions
+
+    Code
+      susc_outbreak_raw
+    Output
+      `epichains` object
+
+      < tree head (from first known ancestor) >
+
+      [1] sim_id     ancestor   generation time      
+      <0 rows> (or 0-length row.names)
+
+      < tree tail >
+
+        sim_id ancestor generation time
+      1      1       NA          1    0
+      Number of ancestors (known): 0
+      Number of generations: 1
+      Use `as.data.frame(<object_name>)` to view the full output in the console.
+
+---
+
+    Code
+      susc_outbreak_raw2
+    Output
+      `epichains` object
+
+      < tree head (from first known ancestor) >
+
+        sim_id ancestor generation       time
+      2      2        1          2 21.5834705
+      3      3        1          2  0.3939008
+      4      4        2          3 21.6595273
+
+      < tree tail >
+
+        sim_id ancestor generation       time
+      1      1       NA          1  0.0000000
+      2      2        1          2 21.5834705
+      3      3        1          2  0.3939008
+      4      4        2          3 21.6595273
+      Number of ancestors (known): 2
+      Number of generations: 3
+      Use `as.data.frame(<object_name>)` to view the full output in the console.
+
+---
+
+    Code
+      tree_sim_raw
+    Output
+      `epichains` object
+
+      < tree head (from first known ancestor) >
+
+        chain_id sim_id ancestor generation
+      3        1      2        1          2
+      4        1      3        1          2
+
+      < tree tail >
+
+        chain_id sim_id ancestor generation
+      1        1      1       NA          1
+      2        2      1       NA          1
+      3        1      2        1          2
+      4        1      3        1          2
+      Chains simulated: 2
+      Number of ancestors (known): 1
+      Number of generations: 2
+      Use `as.data.frame(<object_name>)` to view the full output in the console.
+
+---
+
+    Code
+      tree_sim_raw2
+    Output
+      `epichains` object
+
+      < tree head (from first known ancestor) >
+
+         chain_id sim_id ancestor generation time
+      11        1      2        1          2    3
+      13        2      2        1          2    3
+      15        3      2        1          2    3
+      17        4      2        1          2    3
+      19        6      2        1          2    3
+      20        7      2        1          2    3
+
+      < tree tail >
+
+          chain_id sim_id ancestor generation time
+      92         9     19        8          4    9
+      109        6     19        8          5   12
+      93         9     20        9          4    9
+      110        6     20        9          5   12
+      94         9     21        9          4    9
+      111        6     21        9          5   12
+      Chains simulated: 10
+      Number of ancestors (known): 9
+      Number of generations: 5
+      Use `as.data.frame(<object_name>)` to view the full output in the console.
+
+---
+
+    Code
+      chain_summary_raw
+    Output
+      `epichains` object 
+
+      [1] 4 1
+
+       Simulated chain lengths: 
+
+      Max: 4
+      Min: 1
+
+# head and tail print output as expected
+
+    Code
+      head(susc_outbreak_raw)
+    Output
+      < tree head (from first known ancestor) >
+
+      [1] sim_id     ancestor   generation time      
+      <0 rows> (or 0-length row.names)
+
+---
+
+    Code
+      head(susc_outbreak_raw2)
+    Output
+      < tree head (from first known ancestor) >
+
+        sim_id ancestor generation       time
+      2      2        1          2 21.5834705
+      3      3        1          2  0.3939008
+      4      4        2          3 21.6595273
+
+---
+
+    Code
+      head(tree_sim_raw)
+    Output
+      < tree head (from first known ancestor) >
+
+        chain_id sim_id ancestor generation
+      3        1      2        1          2
+      4        1      3        1          2
+
+---
+
+    Code
+      head(tree_sim_raw2)
+    Output
+      < tree head (from first known ancestor) >
+
+         chain_id sim_id ancestor generation time
+      11        1      2        1          2    3
+      13        2      2        1          2    3
+      15        3      2        1          2    3
+      17        4      2        1          2    3
+      19        6      2        1          2    3
+      20        7      2        1          2    3
+
+---
+
+    Code
+      tail(susc_outbreak_raw)
+    Output
+
+      < tree tail >
+
+        sim_id ancestor generation time
+      1      1       NA          1    0
+
+---
+
+    Code
+      tail(susc_outbreak_raw2)
+    Output
+
+      < tree tail >
+
+        sim_id ancestor generation       time
+      1      1       NA          1  0.0000000
+      2      2        1          2 21.5834705
+      3      3        1          2  0.3939008
+      4      4        2          3 21.6595273
+
+---
+
+    Code
+      tail(tree_sim_raw)
+    Output
+
+      < tree tail >
+
+        chain_id sim_id ancestor generation
+      1        1      1       NA          1
+      2        2      1       NA          1
+      3        1      2        1          2
+      4        1      3        1          2
+
+---
+
+    Code
+      tail(tree_sim_raw2)
+    Output
+
+      < tree tail >
+
+          chain_id sim_id ancestor generation time
+      92         9     19        8          4    9
+      109        6     19        8          5   12
+      93         9     20        9          4    9
+      110        6     20        9          5   12
+      94         9     21        9          4    9
+      111        6     21        9          5   12
+

tests/testthat/test-checks.R

@@ -0,0 +1,18 @@
+test_that("Checks work", {
+  expect_error(
+    check_offspring_valid(1),
+    "character string"
+  )
+  expect_error(
+    check_offspring_func_valid("rrpois"),
+    "does not exist"
+  )
+  expect_error(
+    check_serial_valid("a"),
+    "must be a function"
+  )
+  expect_error(
+    check_nchains_valid(1.1),
+    "less than"
+  )
+})