Compute Marginal Resistance per Pathogen and Antibiotic Class

Collapses drug-level susceptibility data to antibiotic-class level per isolate (\(R_{e,k,c} = 1\) if resistant to any drug in class \(c\)), then computes marginal resistance for every pathogen x class combination found in the data.

Usage

compute_marginal_resistance(
  data,
  pathogen_col = "organism_name",
  org_group_col = "org_group",
  isolate_col = "isolate_id",
  antibiotic_class_col = "antibiotic_class",
  antibiotic_value_col = "antibiotic_value",
  zero_threshold = 0,
  min_n_tested = 30,
  facility_col = NULL,
  facility_name = NULL,
  outcome_col = NULL,
  outcome_value = NULL
)

Arguments

data

Data frame. Pre-processed AMR data at isolate x antibiotic level (one row per isolate-antibiotic combination). Results must already be binary ("S" / "R"); no reclassification is applied.

pathogen_col

Character. Column with pathogen names. Default "organism_name".

org_group_col

Character. Column with organism group labels. Default "org_group".

isolate_col

Character. Column uniquely identifying each isolate. Default "isolate_id".

antibiotic_class_col

Character. Column with the antibiotic class for each drug. Default "antibiotic_class".

antibiotic_value_col

Character. Column with susceptibility result ("S" or "R"). Default "antibiotic_value".

zero_threshold

Numeric. Classes with marginal_resistance <= zero_threshold are listed in $near_zero. Default 0.

min_n_tested

Integer or NULL. Minimum number of isolates that must have been tested for a pathogen-class combination to be retained. Combinations with n_tested < min_n_tested are dropped from $marginal and from $class_long, so the exclusion propagates automatically into compute_pairwise_coresistance() and compute_resistance_profiles(). Set to NULL or 0 to disable the filter. Default 30.

facility_col

Character or NULL. Name of the column identifying the facility/site. When provided together with facility_name, data are filtered to the specified facility before any computation. Both facility_col and facility_name must be supplied together or both left NULL. When provided, facility_col is also retained in $class_long and $marginal so that downstream steps can apply the same filter. Default NULL.

facility_name

Character or NULL. The facility value to retain (matched via == against facility_col). Default NULL.

outcome_col

Character or NULL. Name of the column containing patient outcomes (e.g. "final_outcome"). When provided together with outcome_value, data are filtered to isolates with the specified outcome before any computation. Both outcome_col and outcome_value must be supplied together or both left NULL. When provided, outcome_col is retained in $class_long and $marginal so that downstream steps can apply the same filter. Default NULL.

outcome_value

Character or NULL. The outcome value to retain (e.g. "discharged", "dead"; matched via == against outcome_col). Default NULL.

Value

Named list:

marginal

Data frame with columns: pathogen_col, org_group_col, antibiotic_class_col, n_tested, n_resistant, marginal_resistance. Sorted descending by marginal_resistance within each pathogen.

near_zero

Subset of marginal where marginal_resistance <= zero_threshold. These classes are candidates for exclusion in downstream profiling.

class_long

Collapsed isolate x pathogen x class data frame (columns: isolate_col, pathogen_col, org_group_col, antibiotic_class_col, class_result). Pass this directly to compute_pairwise_coresistance().

Details

Classes whose marginal resistance is at or below zero_threshold are listed in $near_zero as a flag for downstream use – they are not removed here.

Examples

if (FALSE) { # \dontrun{
marg <- compute_marginal_resistance(
  data                 = amr_clean,
  pathogen_col         = "organism_name",
  org_group_col        = "org_group",
  isolate_col          = "isolate_id",
  antibiotic_class_col = "antibiotic_class",
  antibiotic_value_col = "antibiotic_value"
)

marg$marginal # full marginal resistance table
marg$near_zero # classes flagged as near-zero
} # }