mcmodule (version 1.2.0)

trial_totals: Trial Probability and Expected Counts

Description

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 = NULL,
  keep_variates = FALSE,
  summary = TRUE,
  data_name = NULL
)

Value

Updated mcmodule object containing combined node probabilities and probabilities/counts at trial, subset, and set levels.

Arguments

mcmodule

(mcmodule object). Module containing input data and node structure.

mc_names

(character vector). Node names to process.

trials_n

(character). Trial count column name.

subsets_n

(character, optional). Subset count column name. Default: NULL.

subsets_p

(character, optional). Subset prevalence column name. Default: NULL.

name

(character, optional). Custom name for output nodes. Default: NULL.

prefix

(character, optional). Prefix for output node names. Default: NULL.

combine_prob

(logical). If TRUE, combine probability of all nodes assuming independence. Default: TRUE.

all_suffix

(character). Suffix for combined node name. Default: "all".

level_suffix

(list, optional). Suffixes for each hierarchical level. Default: c(trial="trial", subset="subset", set="set").

mctable

(data frame, optional). Monte Carlo nodes definitions. Default: set_mctable().

agg_keys

(character vector, optional). Column names for aggregation. Default: NULL.

agg_suffix

(character). Suffix for aggregated node names. Default: "hag".

keep_variates

(logical). If TRUE, preserve individual variate values. Default: FALSE.

summary

(logical). If TRUE, include summary statistics. Default: TRUE.

data_name

(character, optional). Data name used to create trials_n, subsets_n and subsets_p nodes if they don't exist in mcmodule. Default: NULL.

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)