Calculates probabilities and expected counts across hierarchical levels (trial, subset, set) in a structured population. Uses trial probabilities and handles nested sampling with conditional probabilities.
Usage
trial_totals(
mcmodule,
mc_names,
trials_n,
subsets_n = NULL,
subsets_p = NULL,
name = NULL,
prefix = NULL,
combine_prob = TRUE,
all_suffix = NULL,
level_suffix = c(trial = "trial", subset = "subset", set = "set"),
mctable = set_mctable(),
agg_keys = NULL,
agg_suffix = "agg",
keep_variates = FALSE,
summary = TRUE
)Arguments
- mcmodule
mcmodule object containing input data and node structure
- mc_names
Vector of node names to process
- trials_n
Trial count column name
- subsets_n
Subset count column name (optional)
- subsets_p
Subset prevalence column name (optional)
- name
Custom name for output nodes (optional)
- prefix
Prefix for output node names (optional)
- combine_prob
Combine probability of all nodes assuming independence (default: TRUE)
- all_suffix
Suffix for combined node name (default: "all")
- level_suffix
A list of suffixes for each hierarchical level (default: c(trial="trial",subset="subset",set="set"))
- mctable
Data frame containing Monte Carlo nodes definitions (default: set_mctable())
- agg_keys
Column names for aggregation (optional)
- agg_suffix
Suffix for aggregated node names (default: "agg")
- keep_variates
whether to preserve individual values (default: FALSE)
- summary
Include summary statistics if TRUE (default: TRUE)
Value
Updated mcmodule object containing:
Combined node probabilities
Probabilities and counts at trial level
Probabilities and counts at subset level
Probabilities and counts at set level
Examples
imports_mcmodule <- trial_totals(
mcmodule = imports_mcmodule,
mc_names = "no_detect_a",
trials_n = "animals_n",
subsets_n = "farms_n",
subsets_p = "h_prev",
mctable = imports_mctable
)
print(imports_mcmodule$node_list$no_detect_a_set$summary)
#> mc_name pathogen origin mean sd Min 2.5%
#> 1 no_detect_a_set a nord 0.3750450 0.020108413 0.3410136 0.3426586
#> 2 no_detect_a_set a south 0.2978174 0.064004187 0.1829532 0.1888451
#> 3 no_detect_a_set a east 0.6025875 0.045383047 0.5218729 0.5261802
#> 4 no_detect_a_set b nord 0.9875566 0.008070346 0.9689414 0.9704140
#> 5 no_detect_a_set b south 0.9594431 0.008275134 0.9437901 0.9446762
#> 6 no_detect_a_set b east 0.9668884 0.020678650 0.9177136 0.9230652
#> 25% 50% 75% 97.5% Max nsv Na's
#> 1 0.3576956 0.3748559 0.3928853 0.4077016 0.4094812 1001 0
#> 2 0.2433367 0.3015970 0.3524411 0.3964220 0.4010001 1001 0
#> 3 0.5639605 0.6023181 0.6424667 0.6752938 0.6794225 1001 0
#> 4 0.9814800 0.9895902 0.9944236 0.9973534 0.9975015 1001 0
#> 5 0.9522929 0.9602068 0.9668934 0.9712431 0.9717516 1001 0
#> 6 0.9523051 0.9715396 0.9847453 0.9916434 0.9921812 1001 0