A pre-evaluated mcmodule object containing simulation results for the illustrative animal-import risk assessment. The module represents two hypothetical pathogens imported from three regions of origin and includes input nodes, intermediate calculations, and the probability that an infected animal is not detected before import.
Format
An object of class mcmodule with the following components:
- data
A named list containing the model input data.
- exp
A named list containing the evaluated model expression.
- node_list
A named list of Monte Carlo input and output nodes with their associated metadata. This includes
w_prev,test_sensi,test_origin,infected,false_neg,no_test, andno_detect.- modules
Character vector identifying the modules represented in the object.
Details
The object is generated from imports_data, imports_data_keys, imports_mctable, and imports_exp. It is provided so that package functions can be demonstrated without rebuilding the model each time.
Examples
imports_mcmodule
#> $data
#> $data$imports_data
#> pathogen origin h_prev_min h_prev_max w_prev_min w_prev_max farms_n
#> 1 a nord 0.08 0.10 0.15 0.2 5
#> 2 a south 0.02 0.05 0.15 0.2 10
#> 3 a east 0.10 0.15 0.15 0.2 7
#> 4 b nord 0.50 0.70 0.45 0.6 5
#> 5 b south 0.25 0.30 0.37 0.4 10
#> 6 b east 0.30 0.50 0.45 0.6 7
#> animals_n_mean animals_n_sd test_origin test_sensi_min test_sensi_mode
#> 1 100 6 sometimes 0.89 0.90
#> 2 130 10 sometimes 0.89 0.90
#> 3 140 12 never 0.89 0.90
#> 4 100 2 always 0.80 0.85
#> 5 130 4 sometimes 0.80 0.85
#> 6 140 3 unknown 0.80 0.85
#> test_sensi_max
#> 1 0.91
#> 2 0.91
#> 3 0.91
#> 4 0.90
#> 5 0.90
#> 6 0.90
#>
#>
#> $exp
#> $exp$imports
#> {
#> infected <- w_prev
#> false_neg <- infected * test_origin * (1 - test_sensi)
#> no_test <- infected * (1 - test_origin)
#> no_detect <- false_neg + no_test
#> }
#>
#>
#> $node_list
#> $node_list$w_prev
#> $node_list$w_prev$type
#> [1] "in_node"
#>
#> $node_list$w_prev$mc_func
#> [1] "runif"
#>
#> $node_list$w_prev$description
#> [1] "Within herd prevalence"
#>
#> $node_list$w_prev$inputs_col
#> [1] "w_prev_min" "w_prev_max"
#>
#> $node_list$w_prev$input_dataset
#> [1] "prevalence_region"
#>
#> $node_list$w_prev$keys
#> [1] "pathogen" "origin"
#>
#> $node_list$w_prev$exp_name
#> [1] "imports"
#>
#> $node_list$w_prev$mc_name
#> [1] "w_prev"
#>
#> $node_list$w_prev$mcnode
#> node mode nsv nsu nva variate min mean median max Nas type outm
#> 1 x numeric 1001 1 6 1 0.15 0.176 0.177 0.2 0 V each
#> 2 x numeric 1001 1 6 2 0.15 0.176 0.176 0.2 0 V each
#> 3 x numeric 1001 1 6 3 0.15 0.175 0.175 0.2 0 V each
#> 4 x numeric 1001 1 6 4 0.45 0.525 0.525 0.6 0 V each
#> 5 x numeric 1001 1 6 5 0.37 0.385 0.385 0.4 0 V each
#> 6 x numeric 1001 1 6 6 0.45 0.524 0.524 0.6 0 V each
#>
#> $node_list$w_prev$data_name
#> [1] "imports_data"
#>
#>
#> $node_list$infected
#> $node_list$infected$type
#> [1] "out_node"
#>
#> $node_list$infected$node_exp
#> [1] "w_prev"
#>
#> $node_list$infected$inputs
#> [1] "w_prev"
#>
#> $node_list$infected$exp_name
#> [1] "imports"
#>
#> $node_list$infected$mc_name
#> [1] "infected"
#>
#> $node_list$infected$keys
#> [1] "pathogen" "origin"
#>
#> $node_list$infected$exp_param
#> [1] "w_prev"
#>
#> $node_list$infected$mcnode
#> node mode nsv nsu nva variate min mean median max Nas type outm
#> 1 x numeric 1001 1 6 1 0.15 0.176 0.177 0.2 0 V each
#> 2 x numeric 1001 1 6 2 0.15 0.176 0.176 0.2 0 V each
#> 3 x numeric 1001 1 6 3 0.15 0.175 0.175 0.2 0 V each
#> 4 x numeric 1001 1 6 4 0.45 0.525 0.525 0.6 0 V each
#> 5 x numeric 1001 1 6 5 0.37 0.385 0.385 0.4 0 V each
#> 6 x numeric 1001 1 6 6 0.45 0.524 0.524 0.6 0 V each
#>
#> $node_list$infected$data_name
#> [1] "imports_data"
#>
#>
#> $node_list$test_origin
#> $node_list$test_origin$type
#> [1] "in_node"
#>
#> $node_list$test_origin$description
#> [1] "Probability of the animals being tested in origin"
#>
#> $node_list$test_origin$inputs_col
#> [1] "test_origin"
#>
#> $node_list$test_origin$input_dataset
#> [1] "prevalence_region"
#>
#> $node_list$test_origin$keys
#> [1] "pathogen" "origin"
#>
#> $node_list$test_origin$exp_name
#> [1] "imports"
#>
#> $node_list$test_origin$mc_name
#> [1] "test_origin"
#>
#> $node_list$test_origin$mcnode
#> node mode nsv nsu nva variate min mean median max Nas type outm
#> 1 x numeric 1 1 6 1 0.5 0.5 0.5 0.5 0 0 each
#> 2 x numeric 1 1 6 2 0.5 0.5 0.5 0.5 0 0 each
#> 3 x numeric 1 1 6 3 0.0 0.0 0.0 0.0 0 0 each
#> 4 x numeric 1 1 6 4 1.0 1.0 1.0 1.0 0 0 each
#> 5 x numeric 1 1 6 5 0.5 0.5 0.5 0.5 0 0 each
#> 6 x numeric 1 1 6 6 0.0 0.0 0.0 0.0 0 0 each
#>
#> $node_list$test_origin$data_name
#> [1] "imports_data"
#>
#>
#> $node_list$test_sensi
#> $node_list$test_sensi$type
#> [1] "in_node"
#>
#> $node_list$test_sensi$mc_func
#> [1] "rpert"
#>
#> $node_list$test_sensi$description
#> [1] "Test sensitivity"
#>
#> $node_list$test_sensi$inputs_col
#> [1] "test_sensi_min" "test_sensi_mode" "test_sensi_max"
#>
#> $node_list$test_sensi$input_dataset
#> [1] "test_sensitivity"
#>
#> $node_list$test_sensi$keys
#> [1] "pathogen"
#>
#> $node_list$test_sensi$exp_name
#> [1] "imports"
#>
#> $node_list$test_sensi$mc_name
#> [1] "test_sensi"
#>
#> $node_list$test_sensi$mcnode
#> node mode nsv nsu nva variate min mean median max Nas type outm
#> 1 x numeric 1001 1 6 1 0.891 0.900 0.900 0.910 0 V each
#> 2 x numeric 1001 1 6 2 0.890 0.900 0.900 0.909 0 V each
#> 3 x numeric 1001 1 6 3 0.890 0.900 0.900 0.909 0 V each
#> 4 x numeric 1001 1 6 4 0.804 0.850 0.850 0.894 0 V each
#> 5 x numeric 1001 1 6 5 0.806 0.850 0.850 0.897 0 V each
#> 6 x numeric 1001 1 6 6 0.806 0.851 0.851 0.894 0 V each
#>
#> $node_list$test_sensi$data_name
#> [1] "imports_data"
#>
#>
#> $node_list$false_neg
#> $node_list$false_neg$function_call
#> [1] TRUE
#>
#> $node_list$false_neg$type
#> [1] "out_node"
#>
#> $node_list$false_neg$node_exp
#> [1] "infected * test_origin * (1 - test_sensi)"
#>
#> $node_list$false_neg$inputs
#> [1] "infected" "test_origin" "test_sensi"
#>
#> $node_list$false_neg$exp_name
#> [1] "imports"
#>
#> $node_list$false_neg$mc_name
#> [1] "false_neg"
#>
#> $node_list$false_neg$keys
#> [1] "pathogen" "origin"
#>
#> $node_list$false_neg$exp_param
#> [1] "infected" "test_origin" "test_sensi"
#>
#> $node_list$false_neg$mcnode
#> node mode nsv nsu nva variate min mean median max Nas type
#> 1 x numeric 1001 1 6 1 0.00707 0.00879 0.00884 0.0107 0 V
#> 2 x numeric 1001 1 6 2 0.00688 0.00878 0.00880 0.0107 0 V
#> 3 x numeric 1001 1 6 3 0.00000 0.00000 0.00000 0.0000 0 V
#> 4 x numeric 1001 1 6 4 0.05007 0.07882 0.07818 0.1104 0 V
#> 5 x numeric 1001 1 6 5 0.01920 0.02879 0.02890 0.0378 0 V
#> 6 x numeric 1001 1 6 6 0.00000 0.00000 0.00000 0.0000 0 V
#> outm
#> 1 each
#> 2 each
#> 3 each
#> 4 each
#> 5 each
#> 6 each
#>
#> $node_list$false_neg$data_name
#> [1] "imports_data"
#>
#>
#> $node_list$no_test
#> $node_list$no_test$function_call
#> [1] TRUE
#>
#> $node_list$no_test$type
#> [1] "out_node"
#>
#> $node_list$no_test$node_exp
#> [1] "infected * (1 - test_origin)"
#>
#> $node_list$no_test$inputs
#> [1] "infected" "test_origin"
#>
#> $node_list$no_test$exp_name
#> [1] "imports"
#>
#> $node_list$no_test$mc_name
#> [1] "no_test"
#>
#> $node_list$no_test$keys
#> [1] "pathogen" "origin"
#>
#> $node_list$no_test$exp_param
#> [1] "infected" "test_origin"
#>
#> $node_list$no_test$mcnode
#> node mode nsv nsu nva variate min mean median max Nas type outm
#> 1 x numeric 1001 1 6 1 0.075 0.0879 0.0883 0.1 0 V each
#> 2 x numeric 1001 1 6 2 0.075 0.0878 0.0881 0.1 0 V each
#> 3 x numeric 1001 1 6 3 0.150 0.1746 0.1748 0.2 0 V each
#> 4 x numeric 1001 1 6 4 0.000 0.0000 0.0000 0.0 0 V each
#> 5 x numeric 1001 1 6 5 0.185 0.1925 0.1926 0.2 0 V each
#> 6 x numeric 1001 1 6 6 0.450 0.5243 0.5238 0.6 0 V each
#>
#> $node_list$no_test$data_name
#> [1] "imports_data"
#>
#>
#> $node_list$no_detect
#> $node_list$no_detect$function_call
#> [1] TRUE
#>
#> $node_list$no_detect$type
#> [1] "out_node"
#>
#> $node_list$no_detect$node_exp
#> [1] "false_neg + no_test"
#>
#> $node_list$no_detect$inputs
#> [1] "false_neg" "no_test"
#>
#> $node_list$no_detect$exp_name
#> [1] "imports"
#>
#> $node_list$no_detect$mc_name
#> [1] "no_detect"
#>
#> $node_list$no_detect$keys
#> [1] "pathogen" "origin"
#>
#> $node_list$no_detect$exp_param
#> [1] "false_neg" "no_test"
#>
#> $node_list$no_detect$mcnode
#> node mode nsv nsu nva variate min mean median max Nas type outm
#> 1 x numeric 1001 1 6 1 0.0821 0.0967 0.0972 0.110 0 V each
#> 2 x numeric 1001 1 6 2 0.0819 0.0966 0.0968 0.110 0 V each
#> 3 x numeric 1001 1 6 3 0.1501 0.1746 0.1748 0.200 0 V each
#> 4 x numeric 1001 1 6 4 0.0501 0.0788 0.0782 0.110 0 V each
#> 5 x numeric 1001 1 6 5 0.2063 0.2213 0.2212 0.237 0 V each
#> 6 x numeric 1001 1 6 6 0.4504 0.5243 0.5238 0.600 0 V each
#>
#> $node_list$no_detect$data_name
#> [1] "imports_data"
#>
#>
#>
#> attr(,"class")
#> [1] "mcmodule"
class(imports_mcmodule)
#> [1] "mcmodule"
names(imports_mcmodule$node_list)
#> [1] "w_prev" "infected" "test_origin" "test_sensi" "false_neg"
#> [6] "no_test" "no_detect"
mc_summary(imports_mcmodule, "no_detect")
#> mc_name pathogen origin mean sd Min 2.5%
#> 1 no_detect a nord 0.09672319 0.007918844 0.08212834 0.08327604
#> 2 no_detect a south 0.09659241 0.007844882 0.08193967 0.08300295
#> 3 no_detect a east 0.17457745 0.014002392 0.15006892 0.15118934
#> 4 no_detect b nord 0.07882384 0.011451563 0.05007489 0.05848176
#> 5 no_detect b south 0.22133183 0.006089013 0.20633320 0.21056531
#> 6 no_detect b east 0.52426066 0.043177508 0.45041178 0.45397775
#> 25% 50% 75% 97.5% Max nsv Na's
#> 1 0.08994074 0.09716583 0.10359879 0.1093953 0.1102474 1001 0
#> 2 0.09005791 0.09680435 0.10291212 0.1093358 0.1103894 1001 0
#> 3 0.16254631 0.17482117 0.18649966 0.1982050 0.1999157 1001 0
#> 4 0.07047387 0.07818301 0.08711637 0.1005788 0.1104362 1001 0
#> 5 0.21665153 0.22117476 0.22593424 0.2327192 0.2370769 1001 0
#> 6 0.48702148 0.52379528 0.56172396 0.5970621 0.5999985 1001 0