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Calculate Probabilities and Expected Counts Across Hierarchical Levels

Source: R/totals.R
trial_totals.Rd

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,
  mctable = set_mctable(),
  agg_keys = NULL,
  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

Process all nodes if TRUE (default)

mctable

Data frame containing Monte Carlo nodes definitions (default: set_mctable())

agg_keys

Column names for aggregation (optional)

suffix

Suffix for aggregated names (default: "agg")

keep_variates

whether to preserve individual values (default: FALSE)

summary

Include summary statistics if TRUE (default)

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 0.3751019 0.019789800 0.3408802 0.3428733
#> 2 no_detect_a_set        a  south 0.2952493 0.063365388 0.1831839 0.1887273
#> 3 no_detect_a_set        a   east 0.6072974 0.045790740 0.5217925 0.5254801
#> 4 no_detect_a_set        b   nord 0.9873207 0.008134035 0.9686790 0.9703136
#> 5 no_detect_a_set        b  south 0.9589867 0.007988016 0.9436867 0.9446953
#> 6 no_detect_a_set        b   east 0.9661267 0.021386374 0.9176546 0.9225663
#>         25%       50%       75%     97.5%       Max  nsv Na's
#> 1 0.3576659 0.3746006 0.3927420 0.4074480 0.4094135 1001    0
#> 2 0.2397273 0.2961064 0.3496624 0.3961052 0.4012000 1001    0
#> 3 0.5675934 0.6116438 0.6478969 0.6757313 0.6793628 1001    0
#> 4 0.9813778 0.9891075 0.9943813 0.9972351 0.9975596 1001    0
#> 5 0.9525700 0.9593445 0.9657100 0.9712939 0.9717407 1001    0
#> 6 0.9505468 0.9715490 0.9848100 0.9917126 0.9921561 1001    0