Running ‘tinytest.R’ [46s/55s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  + 
  +   test_tmat_matches_expected <- function(tmat) {
  +     # Check for out of bounds values
  +     tinytest::expect_false(any(tmat < 0))
  +     tinytest::expect_false(any(tmat > 1))
  +   }
  + 
  +   tinytest::test_package("epiworldR")
  + }
  Thank you for using epiworldR! Please consider citing it in your work.
  You can find the citation information by running
    citation("epiworldR")
  
  test-agents-and-dist-virus-tool.R    0 tests    
  test-agents-and-dist-virus-tool.R    0 tests    _________________________________________________________________________
  Running the model...
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
  test-agents-and-dist-virus-tool.R    0 tests    
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  test-agents-and-dist-virus-tool.R    1 tests [0;32mOK[0m Starting multiple runs (100) using 2 thread(s)
  _________________________________________________________________________
  _________________________________________________________________________
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
  test-agents-and-dist-virus-tool.R    1 tests [0;32mOK[0m 
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  test-agents-and-dist-virus-tool.R    2 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    2 tests [0;32mOK[0m _________________________________________________________________________
  Running the model...
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
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  test-agents-and-dist-virus-tool.R    4 tests [0;32mOK[0m Starting multiple runs (100) using 2 thread(s)
  _________________________________________________________________________
  _________________________________________________________________________
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
  test-agents-and-dist-virus-tool.R    4 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    4 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    4 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    5 tests [0;32mOK[0m 
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  test-agents-and-dist-virus-tool.R    5 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    5 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    5 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    5 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    5 tests [0;32mOK[0m _________________________________________________________________________
  Running the model...
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
  test-agents-and-dist-virus-tool.R    5 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    5 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    6 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    6 tests [0;32mOK[0m Starting multiple runs (100) using 2 thread(s)
  _________________________________________________________________________
  _________________________________________________________________________
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
  test-agents-and-dist-virus-tool.R    6 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    6 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    6 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    6 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    7 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    7 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    7 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    7 tests [0;32mOK[0m _________________________________________________________________________
  Running the model...
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
  test-agents-and-dist-virus-tool.R    7 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    7 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    8 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    9 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    9 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    9 tests [0;32mOK[0m Starting multiple runs (100) using 2 thread(s)
  _________________________________________________________________________
  _________________________________________________________________________
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
  test-agents-and-dist-virus-tool.R    9 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    9 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R    9 tests [0;32mOK[0m 
  test-agents-and-dist-virus-tool.R   10 tests [0;32mOK[0m [0;34m5.7s[0m
  
  test-diffnet.R................    0 tests    
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  test-diffnet.R................   12 tests [0;32mOK[0m [0;36m13ms[0m
  
  test-get.R....................    0 tests    
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  test-get.R....................    6 tests [0;32mOK[0m 
  test-get.R....................    6 tests [0;32mOK[0m [0;36m14ms[0m
  
  test-lfmcmc.R.................    0 tests    
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  test-lfmcmc.R.................   63 tests [0;32mOK[0m 
  test-lfmcmc.R.................   64 tests [0;32mOK[0m 
  test-lfmcmc.R.................   65 tests [0;32mOK[0m 
  test-lfmcmc.R.................   66 tests [0;32mOK[0m 
  test-lfmcmc.R.................   67 tests [0;32mOK[0m 
  test-lfmcmc.R.................   68 tests [0;32mOK[0m 
  test-lfmcmc.R.................   69 tests [0;32mOK[0m 
  test-lfmcmc.R.................   70 tests [0;32mOK[0m 
  test-lfmcmc.R.................   71 tests [0;32mOK[0m 
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  test-lfmcmc.R.................   80 tests [0;32mOK[0m 
  test-lfmcmc.R.................   81 tests [0;32mOK[0m 
  test-lfmcmc.R.................   82 tests [0;32mOK[0m [0;34m31.0s[0m
  
  test-measles-quarantine-errors.R    0 tests    
  test-measles-quarantine-errors.R    1 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    2 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    2 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    3 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    4 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    5 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    6 tests [0;32mOK[0m 
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  test-measles-quarantine-errors.R    9 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    9 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    9 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    9 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R    9 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   10 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   11 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   12 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   13 tests [0;32mOK[0m 
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  test-measles-quarantine-errors.R   22 tests [0;32mOK[0m 
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  test-measles-quarantine-errors.R   26 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   27 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   28 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   29 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   30 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   31 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   32 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   33 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   34 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   35 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   36 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   37 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   38 tests [0;32mOK[0m 
  test-measles-quarantine-errors.R   39 tests [0;32mOK[0m [0;36m78ms[0m
  
  test-measles-quarantine-math.R    0 tests    Starting multiple runs (200) using 2 thread(s)
  _________________________________________________________________________
  _________________________________________________________________________
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  ----- PASSED      : test-measles-quarantine-math.R<4--39>
   call| expect_equal(r0_obs, R0, tolerance = 0.1) 
  Starting multiple runs (200) using 2 thread(s)
  _________________________________________________________________________
  _________________________________________________________________________
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  ----- PASSED      : test-measles-quarantine-math.R<4--39>
   call| expect_equal(r0_obs, R0, tolerance = 0.1) 
  Starting multiple runs (200) using 2 thread(s)
  _________________________________________________________________________
  _________________________________________________________________________
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  ----- PASSED      : test-measles-quarantine-math.R<4--39>
   call| expect_equal(r0_obs, R0, tolerance = 0.1) 
  
  test-measles-quarantine-math.R    3 tests [0;32mOK[0m [0;34m6.2s[0m
  
  test-measlesmixing.R..........    0 tests    
  test-measlesmixing.R..........    0 tests    
  test-measlesmixing.R..........    0 tests    
  test-measlesmixing.R..........    0 tests    
  test-measlesmixing.R..........    0 tests    
  test-measlesmixing.R..........    0 tests    
  test-measlesmixing.R..........    0 tests    
  test-measlesmixing.R..........    0 tests    _________________________________________________________________________
  Running the model...
  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
  
  test-measlesmixing.R..........    0 tests    ________________________________________________________________________________
  ________________________________________________________________________________
  SIMULATION STUDY
  
  Name of the model   : Measles with Mixing and Quarantine
  Population size     : 9000
  Agents' data        : (none)
  Number of entities  : 3
  Days (duration)     : 100 (of 100)
  Number of viruses   : 1
  Last run elapsed t  : 241.00ms
  Last run speed      : 3.73 million agents x day / second
  Rewiring            : off
  
  Global events:
   - Update infected individuals (runs daily)
  
  Virus(es):
   - Measles
  
  Tool(s):
   - Vaccine
  
  Model parameters:
   - (IGNORED) Vax improved recovery : 0.8000
   - Contact rate                    : 15.0000
   - Contact tracing days prior      : 4.0000
   - Contact tracing success rate    : 0.8000
   - Days undetected                 : 2.0000
   - Hospitalization period          : 10.0000
   - Hospitalization rate            : 0.1000
   - Incubation period               : 10.0000
   - Isolation period                : 10.0000
   - Isolation willingness           : 0.8000
   - Prodromal period                : 3.0000
   - Quarantine period               : 14.0000
   - Quarantine willingness          : 0.9000
   - Rash period                     : 7.0000
   - Transmission rate               : 0.9000
   - Vaccination rate                : 0.9500
   - Vax efficacy                    : 0.9700
  
  Distribution of the population at time 100:
    - ( 0) Susceptible             : 8999 -> 8999
    - ( 1) Exposed                 :    1 -> 0
    - ( 2) Prodromal               :    0 -> 0
    - ( 3) Rash                    :    0 -> 0
    - ( 4) Isolated                :    0 -> 0
    - ( 5) Isolated Recovered      :    0 -> 0
    - ( 6) Detected Hospitalized   :    0 -> 0
    - ( 7) Quarantined Exposed     :    0 -> 0
    - ( 8) Quarantined Susceptible :    0 -> 0
    - ( 9) Quarantined Prodromal   :    0 -> 0
    - (10) Quarantined Recovered   :    0 -> 0
    - (11) Hospitalized            :    0 -> 0
    - (12) Recovered               :    0 -> 1
  
  Transition Probabilities:
   - Susceptible              1.00  0.00     -     -     -     -     -     -     -     -     -     -     -
   - Exposed                     -  0.96  0.04     -     -     -     -     -     -     -     -     -     -
   - Prodromal                   -     -     -  1.00     -     -     -     -     -     -     -     -     -
   - Rash                        -     -     -     -     -  1.00     -     -     -     -     -     -     -
   - Isolated                    -     -     -     -     -     -     -     -     -     -     -     -     -
   - Isolated Recovered          -     -     -     -     -  0.89     -     -     -     -     -     -  0.11
   - Detected Hospitalized       -     -     -     -     -     -     -     -     -     -     -     -     -
   - Quarantined Exposed         -     -     -     -     -     -     -     -     -     -     -     -     -
   - Quarantined Susceptible     -     -     -     -     -     -     -     -     -     -     -     -     -
   - Quarantined Prodromal       -     -     -     -     -     -     -     -     -     -     -     -     -
   - Quarantined Recovered       -     -     -     -     -     -     -     -     -     -     -     -     -
   - Hospitalized                -     -     -     -     -     -     -     -     -     -     -     -     -
   - Recovered                   -     -     -     -     -     -     -     -     -     -     -     -  1.00
  
  
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  test-measlesmixingriskquarantine.R    0 tests    ________________________________________________________________________________
  ________________________________________________________________________________
  SIMULATION STUDY
  
  Name of the model   : Measles with Mixing and Risk-based Quarantine
  Population size     : 9000
  Agents' data        : (none)
  Number of entities  : 3
  Days (duration)     : 100 (of 100)
  Number of viruses   : 1
  Last run elapsed t  : 213.00ms
  Last run speed      : 4.22 million agents x day / second
  Rewiring            : off
  
  Global events:
   - Update infected individuals (runs daily)
  
  Virus(es):
   - Measles
  
  Tool(s):
   - Vaccine
  
  Model parameters:
   - Contact rate                 : 15.0000
   - Contact tracing days prior   : 4.0000
   - Contact tracing success rate : 0.8000
   - Days undetected              : 2.0000
   - Detection rate quarantine    : 0.5000
   - Hospitalization period       : 10.0000
   - Hospitalization rate         : 0.1000
   - Incubation period            : 10.0000
   - Isolation period             : 10.0000
   - Isolation willingness        : 0.8000
   - Prodromal period             : 3.0000
   - Quarantine period high       : 21.0000
   - Quarantine period low        : 7.0000
   - Quarantine period medium     : 14.0000
   - Quarantine willingness       : 0.9000
   - Rash period                  : 7.0000
   - Transmission rate            : 0.9000
   - Vaccination rate             : 0.9500
   - Vax efficacy                 : 0.9700
  
  Distribution of the population at time 100:
    - ( 0) Susceptible             : 8999 -> 8999
    - ( 1) Exposed                 :    1 -> 0
    - ( 2) Prodromal               :    0 -> 0
    - ( 3) Rash                    :    0 -> 0
    - ( 4) Isolated                :    0 -> 0
    - ( 5) Isolated Recovered      :    0 -> 0
    - ( 6) Detected Hospitalized   :    0 -> 0
    - ( 7) Quarantined Exposed     :    0 -> 0
    - ( 8) Quarantined Susceptible :    0 -> 0
    - ( 9) Quarantined Prodromal   :    0 -> 0
    - (10) Quarantined Recovered   :    0 -> 0
    - (11) Hospitalized            :    0 -> 0
    - (12) Recovered               :    0 -> 1
  
  Transition Probabilities:
   - Susceptible              1.00  0.00     -     -     -     -     -     -  0.00     -     -     -     -
   - Exposed                     -  0.96  0.04     -     -     -     -     -     -     -     -     -     -
   - Prodromal                   -     -     -  1.00     -     -     -     -     -     -     -     -     -
   - Rash                        -     -     -     -     -  1.00     -     -     -     -     -     -     -
   - Isolated                    -     -     -     -     -     -     -     -     -     -     -     -     -
   - Isolated Recovered          -     -     -     -     -  0.89     -     -     -     -     -     -  0.11
   - Detected Hospitalized       -     -     -     -     -     -     -     -     -     -     -     -     -
   - Quarantined Exposed         -     -     -     -     -     -     -     -     -     -     -     -     -
   - Quarantined Susceptible  0.09     -     -     -     -     -     -     -  0.91     -     -     -     -
   - Quarantined Prodromal       -     -     -     -     -     -     -     -     -     -     -     -     -
   - Quarantined Recovered       -     -     -     -     -     -     -     -     -     -     -     -     -
   - Hospitalized                -     -     -     -     -     -     -     -     -     -     -     -     -
   - Recovered                   -     -     -     -     -     -     -     -     -     -     -     -  1.00
  
  
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  test-seirmixing.R.............    0 tests    
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  test-seirmixing.R.............    0 tests    _________________________________________________________________________
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  test-seirmixing.R.............    0 tests    ________________________________________________________________________________
  ________________________________________________________________________________
  SIMULATION STUDY
  
  Name of the model   : Susceptible-Exposed-Infected-Removed (SEIR) with Mixing
  Population size     : 9000
  Agents' data        : (none)
  Number of entities  : 3
  Days (duration)     : 100 (of 100)
  Number of viruses   : 1
  Last run elapsed t  : 174.00ms
  Last run speed      : 5.16 million agents x day / second
  Rewiring            : off
  
  Global events:
   - Update infected individuals (runs daily)
  
  Virus(es):
   - Flu
  
  Tool(s):
   (none)
  
  Model parameters:
   - Avg. Incubation days : 0.0090
   - Contact rate         : 40.0000
   - Prob. Recovery       : 0.1000
   - Prob. Transmission   : 1.0000
  
  Distribution of the population at time 100:
    - (0) Susceptible : 8999 -> 6000
    - (1) Exposed     :    1 -> 0
    - (2) Infected    :    0 -> 0
    - (3) Recovered   :    0 -> 3000
  
  Transition Probabilities:
   - Susceptible  1.00  0.00     -     -
   - Exposed         -     -  1.00     -
   - Infected        -     -  0.90  0.10
   - Recovered       -     -     -  1.00
  
  
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  test-seirmixingquarantine.R...    0 tests    
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  test-seirmixingquarantine.R...    0 tests    _________________________________________________________________________
  Running the model...
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  test-seirmixingquarantine.R...    0 tests    ________________________________________________________________________________
  ________________________________________________________________________________
  SIMULATION STUDY
  
  Name of the model   : SEIR with Mixing and Quarantine
  Population size     : 9000
  Agents' data        : (none)
  Number of entities  : 3
  Days (duration)     : 100 (of 100)
  Number of viruses   : 1
  Last run elapsed t  : 259.00ms
  Last run speed      : 3.47 million agents x day / second
  Rewiring            : off
  
  Global events:
   - Update infected individuals (runs daily)
  
  Virus(es):
   - Flu
  
  Tool(s):
   (none)
  
  Model parameters:
   - Avg. Incubation days         : 0.0090
   - Contact rate                 : 40.0000
   - Contact tracing days prior   : 3.0000
   - Contact tracing success rate : 0.7000
   - Days undetected              : 3.0000
   - Hospitalization period       : 7.0000
   - Hospitalization rate         : 0.0500
   - Isolation period             : 7.0000
   - Isolation willingness        : 0.5000
   - Prob. Recovery               : 0.1000
   - Prob. Transmission           : 1.0000
   - Quarantine period            : 14.0000
   - Quarantine willingness       : 0.8000
  
  Distribution of the population at time 100:
    - ( 0) Susceptible             : 8999 -> 6000
    - ( 1) Exposed                 :    1 -> 0
    - ( 2) Infected                :    0 -> 0
    - ( 3) Isolated                :    0 -> 0
    - ( 4) Detected Hospitalized   :    0 -> 0
    - ( 5) Quarantined Susceptible :    0 -> 0
    - ( 6) Quarantined Exposed     :    0 -> 0
    - ( 7) Isolated Recovered      :    0 -> 0
    - ( 8) Hospitalized            :    0 -> 0
    - ( 9) Recovered               :    0 -> 3000
  
  Transition Probabilities:
   - Susceptible              1.00  0.00     -     -     -     -  0.00     -     -     -
   - Exposed                     -     -  0.92  0.08     -     -     -     -     -     -
   - Infected                    -     -  0.73  0.11  0.02     -     -  0.01  0.03  0.09
   - Isolated                    -     -  0.15  0.71  0.04     -     -  0.08  0.01  0.02
   - Detected Hospitalized       -     -     -     -  0.86     -     -     -     -  0.14
   - Quarantined Susceptible     -     -     -     -     -     -     -     -     -     -
   - Quarantined Exposed         -     -     -  1.00     -     -     -     -     -     -
   - Isolated Recovered          -     -     -     -     -     -     -  0.72     -  0.28
   - Hospitalized                -     -     -     -     -     -     -     -  0.85  0.15
   - Recovered                   -     -     -     -     -     -     -     -     -  1.00
  
  
  test-seirmixingquarantine.R...    0 tests    
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  ----- FAILED[xcpt]: test-model-methods.R<19--22>
   call| expect_message(md_with_output <- draw_mermaid(model, output_file = "mermaid_diagram.txt"), 
   call| -->    "Diagram written")
   diff| No message was emitted
   diff| Found 0 message(s), 0 warning(s), and 1 error(s):
   diff| 
   diff| ERR: Could not open the file mermaid_diagram.txt for writing.
  ----- FAILED[data]: test-model-methods.R<25--25>
   call| expect_true(file.exists("mermaid_diagram.txt"))
   diff| Expected TRUE, got FALSE
  Error: 2 out of 511 tests failed
  In addition: Warning message:
  In file.remove("mermaid_diagram.txt") :
    cannot remove file 'mermaid_diagram.txt', reason 'Read-only file system'
  Execution halted