tests/testthat/_snaps/epichains.md

In epichains: Simulating and Analysing Transmission Chain Statistics Using Branching Process Models

print.epichains works for simulation functions

Code
  susc_outbreak_raw
Output
  `<epichains>` object

  < epichains head (from first known infector) >

     chain infector infectee generation       time
  11     1        1        2          2 58.2546995
  12     2        1        2          2  5.4332994
  13     5        1        2          2  2.0539399
  14     6        1        2          2  0.5332318
  15     6        1        3          2 30.2672618
  16     6        1        4          2  0.1588130


  Number of chains: 10
  Number of infectors (known): 8
  Number of generations: 6
  Use `as.data.frame(<object_name>)` to view the full output in the console.

Code
  susc_outbreak_raw2
Output
  `<epichains>` object

  < epichains head (from first known infector) >

     chain infector infectee generation       time
  11     1        1        2          2  6.5291176
  12     3        1        2          2  4.5366156
  13     4        1        2          2  0.4951176
  14     6        1        2          2  8.9518883
  15     7        1        2          2 20.7565268
  16     8        1        2          2  8.4553011


  Number of chains: 10
  Number of infectors (known): 4
  Number of generations: 4
  Use `as.data.frame(<object_name>)` to view the full output in the console.

Code
  tree_sim_raw
Output
  `<epichains>` object

  < epichains head (from first known infector) >

    chain infector infectee generation
  3     1        1        2          2
  4     2        1        2          2
  5     1        2        3          3
  6     1        2        4          3
  7     2        2        3          3
  8     1        4        5          4


  Number of chains: 2
  Number of infectors (known): 60
  Number of generations: 15
  Use `as.data.frame(<object_name>)` to view the full output in the console.

Code
  tree_sim_raw2
Output
  `<epichains>` object

  < epichains head (from first known infector) >

     chain infector infectee generation      time
  11     1        1        2          2  1.169061
  12     1        1        3          2 14.980844
  13     1        1        4          2  1.417131
  14     2        1        2          2  1.932143
  15     2        1        3          2  6.667853
  16     2        1        4          2  1.127939


  Number of chains: 10
  Number of infectors (known): 9
  Number of generations: 7
  Use `as.data.frame(<object_name>)` to view the full output in the console.

Code
  chain_summary_raw
Output
  `epichains_summary` object

  [1] 15  5

   Simulated lengths:

  Max: 15
  Min: 5

Code
  chain_lengths_with_Infs
Output
  `epichains_summary` object

   [1]   8   2 Inf   8   1 Inf   8 Inf   2   3

   Simulated lengths:

  Max: >=10
  Min: 1

Code
  chain_lengths_all_Infs
Output
  `epichains_summary` object

  [1] Inf Inf

   Simulated lengths:

  Max: >=10
  Min: >=10

head and tail print output as expected

Code
  head(susc_outbreak_raw)
Output
     chain infector infectee generation       time
  11     2        1        2          2 21.1379640
  12     2        1        3          2  8.8063185
  13     4        1        2          2  1.1541073
  14     7        1        2          2  2.0154108
  15     9        1        2          2  0.4662312
  16    10        1        2          2  0.2252704

Code
  head(tree_sim_raw2)
Output
     chain infector infectee generation      time
  11     1        1        2          2 7.3753537
  12     1        1        3          2 2.1907300
  13     1        1        4          2 9.1453972
  14     1        1        5          2 1.0399607
  15     2        1        2          2 3.6495519
  16     3        1        2          2 0.5958979

Code
  tail(susc_outbreak_raw)
Output
     chain infector infectee generation     time
  37     4       15       16          8 32.71635
  38    10        9       10          8 43.00686
  39     4       16       17          9 35.32430
  40     4       17       18         10 39.61216
  41     4       18       19         11 50.06649
  42     4       19       20         12 56.45937

Code
  tail(tree_sim_raw2)
Output
      chain infector infectee generation      time
  137     9        6       13          5 35.299172
  138    10        5        8          5 12.281767
  139    10        6        9          5  8.809650
  140    10        6       10          5  2.532314
  141    10        6       11          5  3.215042
  142    10        7       12          5  5.640260

epichains documentation built on Oct. 14, 2024, 5:10 p.m.