PTBinteRface

This is a wrapper package for INRAE’s PTB model - this can be installed as pre-built binaries from our r-universe repo:

install.packages("PTBinteRface", repos = c('https://ku-awdc.r-universe.dev', 'https://cloud.r-project.org'))

Alternatively, it can be built from source via our drat repository:

install.packages("PTBinteRface", repos = c('https://ku-awdc.github.io/drat/', 'https://cloud.r-project.org'))

After installation, the model can be run using:

library("PTBinteRface")
results <- run_ptb_model()

Information on the parameters is given in the help file for ?run_ptb_model, and examples of the data frame inputs are given in the underlying PTBinraeR package.

The output from the model is a named list of data frames corresponding to the files output by the model:

results
#> $IhPerHerdPerStep_run0.csv
#> # A tibble: 1 × 471
#>      X1    X2    X3    X4    X5    X6    X7    X8    X9   X10   X11   X12   X13
#>   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1     0     0     0     0     0     0     0     0     0     0     0     0     0
#> # ℹ 458 more variables: X14 <dbl>, X15 <dbl>, X16 <dbl>, X17 <dbl>, X18 <dbl>,
#> #   X19 <dbl>, X20 <dbl>, X21 <dbl>, X22 <dbl>, X23 <dbl>, X24 <dbl>,
#> #   X25 <dbl>, X26 <dbl>, X27 <dbl>, X28 <dbl>, X29 <dbl>, X30 <dbl>,
#> #   X31 <dbl>, X32 <dbl>, X33 <dbl>, X34 <dbl>, X35 <dbl>, X36 <dbl>,
#> #   X37 <dbl>, X38 <dbl>, X39 <dbl>, X40 <dbl>, X41 <dbl>, X42 <dbl>,
#> #   X43 <dbl>, X44 <dbl>, X45 <dbl>, X46 <dbl>, X47 <dbl>, X48 <dbl>,
#> #   X49 <dbl>, X50 <dbl>, X51 <dbl>, X52 <dbl>, X53 <dbl>, X54 <dbl>, …
#> 
#> $infected2YOPerHerdPerStep_run0.csv
#> # A tibble: 1 × 471
#>      X1    X2    X3    X4    X5    X6    X7    X8    X9   X10   X11   X12   X13
#>   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1     0     0     0     0     0     0     0     0     0     0     0     0     0
#> # ℹ 458 more variables: X14 <dbl>, X15 <dbl>, X16 <dbl>, X17 <dbl>, X18 <dbl>,
#> #   X19 <dbl>, X20 <dbl>, X21 <dbl>, X22 <dbl>, X23 <dbl>, X24 <dbl>,
#> #   X25 <dbl>, X26 <dbl>, X27 <dbl>, X28 <dbl>, X29 <dbl>, X30 <dbl>,
#> #   X31 <dbl>, X32 <dbl>, X33 <dbl>, X34 <dbl>, X35 <dbl>, X36 <dbl>,
#> #   X37 <dbl>, X38 <dbl>, X39 <dbl>, X40 <dbl>, X41 <dbl>, X42 <dbl>,
#> #   X43 <dbl>, X44 <dbl>, X45 <dbl>, X46 <dbl>, X47 <dbl>, X48 <dbl>,
#> #   X49 <dbl>, X50 <dbl>, X51 <dbl>, X52 <dbl>, X53 <dbl>, X54 <dbl>, …
#> 
#> $persistencePerHerdPerStep_run0.csv
#> # A tibble: 1 × 471
#>      X1    X2    X3    X4    X5    X6    X7    X8    X9   X10   X11   X12   X13
#>   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1     0     0     0     0     0     0     0     0     0     0     0     0     0
#> # ℹ 458 more variables: X14 <dbl>, X15 <dbl>, X16 <dbl>, X17 <dbl>, X18 <dbl>,
#> #   X19 <dbl>, X20 <dbl>, X21 <dbl>, X22 <dbl>, X23 <dbl>, X24 <dbl>,
#> #   X25 <dbl>, X26 <dbl>, X27 <dbl>, X28 <dbl>, X29 <dbl>, X30 <dbl>,
#> #   X31 <dbl>, X32 <dbl>, X33 <dbl>, X34 <dbl>, X35 <dbl>, X36 <dbl>,
#> #   X37 <dbl>, X38 <dbl>, X39 <dbl>, X40 <dbl>, X41 <dbl>, X42 <dbl>,
#> #   X43 <dbl>, X44 <dbl>, X45 <dbl>, X46 <dbl>, X47 <dbl>, X48 <dbl>,
#> #   X49 <dbl>, X50 <dbl>, X51 <dbl>, X52 <dbl>, X53 <dbl>, X54 <dbl>, …
#> 
#> $positiveIhPerHerdPerStep_run0.csv
#> # A tibble: 1 × 471
#>      X1    X2    X3    X4    X5    X6    X7    X8    X9   X10   X11   X12   X13
#>   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1     0     0     0     0     0     0     0     0     0     0     0     0     0
#> # ℹ 458 more variables: X14 <dbl>, X15 <dbl>, X16 <dbl>, X17 <dbl>, X18 <dbl>,
#> #   X19 <dbl>, X20 <dbl>, X21 <dbl>, X22 <dbl>, X23 <dbl>, X24 <dbl>,
#> #   X25 <dbl>, X26 <dbl>, X27 <dbl>, X28 <dbl>, X29 <dbl>, X30 <dbl>,
#> #   X31 <dbl>, X32 <dbl>, X33 <dbl>, X34 <dbl>, X35 <dbl>, X36 <dbl>,
#> #   X37 <dbl>, X38 <dbl>, X39 <dbl>, X40 <dbl>, X41 <dbl>, X42 <dbl>,
#> #   X43 <dbl>, X44 <dbl>, X45 <dbl>, X46 <dbl>, X47 <dbl>, X48 <dbl>,
#> #   X49 <dbl>, X50 <dbl>, X51 <dbl>, X52 <dbl>, X53 <dbl>, X54 <dbl>, …
#> 
#> $statesPerHerdPerStep_run0.csv
#> # A tibble: 1 × 471
#>      X1    X2    X3    X4    X5    X6    X7    X8    X9   X10   X11   X12   X13
#>   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1     0     0     0     0     0     0     0     0     0     0     0     0     0
#> # ℹ 458 more variables: X14 <dbl>, X15 <dbl>, X16 <dbl>, X17 <dbl>, X18 <dbl>,
#> #   X19 <dbl>, X20 <dbl>, X21 <dbl>, X22 <dbl>, X23 <dbl>, X24 <dbl>,
#> #   X25 <dbl>, X26 <dbl>, X27 <dbl>, X28 <dbl>, X29 <dbl>, X30 <dbl>,
#> #   X31 <dbl>, X32 <dbl>, X33 <dbl>, X34 <dbl>, X35 <dbl>, X36 <dbl>,
#> #   X37 <dbl>, X38 <dbl>, X39 <dbl>, X40 <dbl>, X41 <dbl>, X42 <dbl>,
#> #   X43 <dbl>, X44 <dbl>, X45 <dbl>, X46 <dbl>, X47 <dbl>, X48 <dbl>,
#> #   X49 <dbl>, X50 <dbl>, X51 <dbl>, X52 <dbl>, X53 <dbl>, X54 <dbl>, …
#> 
#> $statusPerHerdPerStep_run0.csv
#> # A tibble: 0 × 0
#> 
#> $twoYearsOldPerHerdPerStep_run0.csv
#> # A tibble: 1 × 471
#>      X1    X2    X3    X4    X5    X6    X7    X8    X9   X10   X11   X12   X13
#>   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1    43    43    43    43    43    43    43    43    42    42    42    42    42
#> # ℹ 458 more variables: X14 <dbl>, X15 <dbl>, X16 <dbl>, X17 <dbl>, X18 <dbl>,
#> #   X19 <dbl>, X20 <dbl>, X21 <dbl>, X22 <dbl>, X23 <dbl>, X24 <dbl>,
#> #   X25 <dbl>, X26 <dbl>, X27 <dbl>, X28 <dbl>, X29 <dbl>, X30 <dbl>,
#> #   X31 <dbl>, X32 <dbl>, X33 <dbl>, X34 <dbl>, X35 <dbl>, X36 <dbl>,
#> #   X37 <dbl>, X38 <dbl>, X39 <dbl>, X40 <dbl>, X41 <dbl>, X42 <dbl>,
#> #   X43 <dbl>, X44 <dbl>, X45 <dbl>, X46 <dbl>, X47 <dbl>, X48 <dbl>,
#> #   X49 <dbl>, X50 <dbl>, X51 <dbl>, X52 <dbl>, X53 <dbl>, X54 <dbl>, …