tests/testthat/_snaps/parameter_tbl.md

In epiparameter: Classes and Helper Functions for Working with Epidemiological Parameters

parameter_tbl works as expected supplied with db

Code
  dist_tbl
Output
  # Parameter table:
  # A data frame:    125 x 7
     disease          pathogen epi_name prob_distribution author  year sample_size
     <chr>            <chr>    <chr>    <chr>             <chr>  <dbl>       <dbl>
   1 Adenovirus       Adenovi~ incubat~ lnorm             Lessl~  2009          14
   2 Human Coronavir~ Human_C~ incubat~ lnorm             Lessl~  2009          13
   3 SARS             SARS-Co~ incubat~ lnorm             Lessl~  2009         157
   4 Influenza        Influen~ incubat~ lnorm             Lessl~  2009         151
   5 Influenza        Influen~ incubat~ lnorm             Lessl~  2009          90
   6 Influenza        Influen~ incubat~ lnorm             Lessl~  2009          78
   7 Measles          Measles~ incubat~ lnorm             Lessl~  2009          55
   8 Parainfluenza    Parainf~ incubat~ lnorm             Lessl~  2009          11
   9 RSV              RSV      incubat~ lnorm             Lessl~  2009          24
  10 Rhinovirus       Rhinovi~ incubat~ lnorm             Lessl~  2009          28
  # i 115 more rows

parameter_tbl works for incubation period with db

Code
  incub_tbl
Output
  # Parameter table:
  # A data frame:    73 x 7
     disease          pathogen epi_name prob_distribution author  year sample_size
     <chr>            <chr>    <chr>    <chr>             <chr>  <dbl>       <dbl>
   1 Adenovirus       Adenovi~ incubat~ lnorm             Lessl~  2009          14
   2 Human Coronavir~ Human_C~ incubat~ lnorm             Lessl~  2009          13
   3 SARS             SARS-Co~ incubat~ lnorm             Lessl~  2009         157
   4 Influenza        Influen~ incubat~ lnorm             Lessl~  2009         151
   5 Influenza        Influen~ incubat~ lnorm             Lessl~  2009          90
   6 Influenza        Influen~ incubat~ lnorm             Lessl~  2009          78
   7 Measles          Measles~ incubat~ lnorm             Lessl~  2009          55
   8 Parainfluenza    Parainf~ incubat~ lnorm             Lessl~  2009          11
   9 RSV              RSV      incubat~ lnorm             Lessl~  2009          24
  10 Rhinovirus       Rhinovi~ incubat~ lnorm             Lessl~  2009          28
  # i 63 more rows

parameter_tbl works for different distribution with db

Code
  serial_tbl
Output
  # Parameter table:
  # A data frame:    18 x 7
     disease          pathogen epi_name prob_distribution author  year sample_size
     <chr>            <chr>    <chr>    <chr>             <chr>  <dbl>       <dbl>
   1 Influenza        Influen~ serial ~ gamma             Ghani~  2009          58
   2 Marburg Virus D~ Marburg~ serial ~ <NA>              Pavlin  2014          38
   3 Marburg Virus D~ Marburg~ serial ~ gamma             Ajell~  2012         374
   4 Mpox             Mpox Vi~ serial ~ gamma             Madew~  2022          57
   5 Mpox             Mpox Vi~ serial ~ gamma             Madew~  2022          40
   6 Ebola Virus Dis~ Ebola V~ serial ~ gamma             WHO E~  2015         305
   7 Ebola Virus Dis~ Ebola V~ serial ~ gamma             WHO E~  2015          37
   8 Ebola Virus Dis~ Ebola V~ serial ~ gamma             WHO E~  2015         147
   9 Ebola Virus Dis~ Ebola V~ serial ~ gamma             WHO E~  2015         112
  10 MERS             MERS-Cov serial ~ lnorm             Assir~  2013          23
  11 MERS             MERS-Cov serial ~ gamma             Cowli~  2015          99
  12 COVID-19         SARS-Co~ serial ~ <NA>              Alene~  2021        3924
  13 COVID-19         SARS-Co~ serial ~ lnorm             Nishi~  2020          28
  14 COVID-19         SARS-Co~ serial ~ weibull           Nishi~  2020          18
  15 COVID-19         SARS-Co~ serial ~ norm              Yang ~  2020         131
  16 Mpox             Mpox Vi~ serial ~ gamma             Guo e~  2022          42
  17 Mpox             Mpox Vi~ serial ~ <NA>              Wang ~  2022          16
  18 Mpox             Mpox Vi~ serial ~ <NA>              Wang ~  2022          34

parameter_tbl works for COVID-19 db

Code
  incub_tbl
Output
  # Parameter table:
  # A data frame:    27 x 7
     disease  pathogen   epi_name       prob_distribution author  year sample_size
     <chr>    <chr>      <chr>          <chr>             <chr>  <dbl>       <dbl>
   1 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Men e~  2020          59
   2 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Rai e~  2022        6241
   3 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Alene~  2021        1453
   4 COVID-19 SARS-CoV-2 serial interv~ <NA>              Alene~  2021        3924
   5 COVID-19 SARS-CoV-2 serial interv~ lnorm             Nishi~  2020          28
   6 COVID-19 SARS-CoV-2 serial interv~ weibull           Nishi~  2020          18
   7 COVID-19 SARS-CoV-2 incubation pe~ weibull           Yang ~  2020         178
   8 COVID-19 SARS-CoV-2 serial interv~ norm              Yang ~  2020         131
   9 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Elias~  2021       28675
  10 COVID-19 SARS-CoV-2 incubation pe~ weibull           Bui e~  2020          19
  # i 17 more rows

parameter_tbl works for SARS-CoV-2 db

Code
  incub_tbl
Output
  # Parameter table:
  # A data frame:    27 x 7
     disease  pathogen   epi_name       prob_distribution author  year sample_size
     <chr>    <chr>      <chr>          <chr>             <chr>  <dbl>       <dbl>
   1 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Men e~  2020          59
   2 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Rai e~  2022        6241
   3 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Alene~  2021        1453
   4 COVID-19 SARS-CoV-2 serial interv~ <NA>              Alene~  2021        3924
   5 COVID-19 SARS-CoV-2 serial interv~ lnorm             Nishi~  2020          28
   6 COVID-19 SARS-CoV-2 serial interv~ weibull           Nishi~  2020          18
   7 COVID-19 SARS-CoV-2 incubation pe~ weibull           Yang ~  2020         178
   8 COVID-19 SARS-CoV-2 serial interv~ norm              Yang ~  2020         131
   9 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Elias~  2021       28675
  10 COVID-19 SARS-CoV-2 incubation pe~ weibull           Bui e~  2020          19
  # i 17 more rows

parameter_tbl works for disease & epi_name subset with db

Code
  incub_tbl
Output
  # Parameter table:
  # A data frame:    15 x 7
     disease  pathogen   epi_name       prob_distribution author  year sample_size
     <chr>    <chr>      <chr>          <chr>             <chr>  <dbl>       <dbl>
   1 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Men e~  2020          59
   2 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Rai e~  2022        6241
   3 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Alene~  2021        1453
   4 COVID-19 SARS-CoV-2 incubation pe~ weibull           Yang ~  2020         178
   5 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Elias~  2021       28675
   6 COVID-19 SARS-CoV-2 incubation pe~ weibull           Bui e~  2020          19
   7 COVID-19 SARS-CoV-2 incubation pe~ lnorm             McAlo~  2020        1357
   8 COVID-19 SARS-CoV-2 incubation pe~ lnorm             McAlo~  2020        1269
   9 COVID-19 SARS-CoV-2 incubation pe~ lnorm             Linto~  2020          52
  10 COVID-19 SARS-CoV-2 incubation pe~ lnorm             Linto~  2020         158
  11 COVID-19 SARS-CoV-2 incubation pe~ lnorm             Linto~  2020          52
  12 COVID-19 SARS-CoV-2 incubation pe~ lnorm             Lauer~  2020         181
  13 COVID-19 SARS-CoV-2 incubation pe~ lnorm             Lauer~  2020          99
  14 COVID-19 SARS-CoV-2 incubation pe~ lnorm             Lauer~  2020         108
  15 COVID-19 SARS-CoV-2 incubation pe~ lnorm             Lauer~  2020          73

parameter_tbl works when supplied a subset db

Code
  covid_tbl
Output
  # Parameter table:
  # A data frame:    27 x 7
     disease  pathogen   epi_name       prob_distribution author  year sample_size
     <chr>    <chr>      <chr>          <chr>             <chr>  <dbl>       <dbl>
   1 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Men e~  2020          59
   2 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Rai e~  2022        6241
   3 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Alene~  2021        1453
   4 COVID-19 SARS-CoV-2 serial interv~ <NA>              Alene~  2021        3924
   5 COVID-19 SARS-CoV-2 serial interv~ lnorm             Nishi~  2020          28
   6 COVID-19 SARS-CoV-2 serial interv~ weibull           Nishi~  2020          18
   7 COVID-19 SARS-CoV-2 incubation pe~ weibull           Yang ~  2020         178
   8 COVID-19 SARS-CoV-2 serial interv~ norm              Yang ~  2020         131
   9 COVID-19 SARS-CoV-2 incubation pe~ <NA>              Elias~  2021       28675
  10 COVID-19 SARS-CoV-2 incubation pe~ weibull           Bui e~  2020          19
  # i 17 more rows

parameter_tbl works as expected supplied with

Code
  dist_tbl
Output
  # Parameter table:
  # A data frame:    1 x 7
    disease  pathogen   epi_name        prob_distribution author  year sample_size
    <chr>    <chr>      <chr>           <chr>             <chr>  <dbl>       <dbl>
  1 COVID-19 SARS-CoV-2 onset to hospi~ lnorm             Linto~  2020         155

parameter_tbl works as expected with discretised

Code
  dist_tbl
Output
  # Parameter table:
  # A data frame:    1 x 7
    disease pathogen epi_name        prob_distribution author  year sample_size
    <chr>   <chr>    <chr>           <chr>             <chr>  <dbl>       <dbl>
  1 Ebola   <NA>     serial interval gamma             Smith   2022          NA

epiparameter documentation built on April 3, 2025, 5:50 p.m.