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Compute Pairwise Co-resistance Matrices per Pathogen

Source: R/resistance.R
compute_pairwise_coresistance.Rd

For every pathogen and every pair of antibiotic classes \((c_i, c_j)\) that were both tested: $$ T_{k,i,j} = \sum_e \mathbf{1}(c_i \text{ tested} \land c_j \text{ tested}) $$ $$ R_{k,i,j} = \sum_e \mathbf{1}(R_{e,k,c_i}=1 \land R_{e,k,c_j}=1) $$ $$ \text{Prev}_{k,i,j} = R_{k,i,j} \;/\; T_{k,i,j} $$

Usage

compute_pairwise_coresistance(
  marginal_output,
  pathogen_col = "organism_name",
  org_group_col = "org_group",
  isolate_col = "isolate_id",
  antibiotic_class_col = "antibiotic_class",
  min_co_tested = 10,
  facility_col = NULL,
  facility_name = NULL,
  outcome_col = NULL,
  outcome_value = NULL
)

Arguments

marginal_output

The list returned by compute_marginal_resistance(). The $class_long element is used as input.

pathogen_col

Character. Must match the column name used in Step 1. Default "organism_name".

org_group_col

Character. Default "org_group".

isolate_col

Character. Default "isolate_id".

antibiotic_class_col

Character. Default "antibiotic_class".

min_co_tested

Integer. Pairwise cells with fewer than min_co_tested co-tested isolates are set to NA in the prevalence matrix. Default 10.

facility_col

Character or NULL. Column identifying the facility/site. When provided together with facility_name, filters class_long to the specified facility before building matrices. For this to work, compute_marginal_resistance() must have been called with the same facility_col argument so that the column is present in $class_long. Both must be supplied together or both left NULL. Default NULL.

facility_name

Character or NULL. Facility value to retain. Default NULL.

outcome_col

Character or NULL. Column containing patient outcomes. When provided together with outcome_value, filters class_long to isolates with the specified outcome before building matrices. compute_marginal_resistance() must have been called with the same outcome_col so that the column is present in $class_long. Both must be supplied together or both left NULL. Default NULL.

outcome_value

Character or NULL. Outcome value to retain (e.g. "discharged", "dead"). Default NULL.

Value

Named list. One entry per pathogen (keyed by pathogen name), each containing:

prevalence

Square symmetric matrix of pairwise co-resistance rates. Diagonal and cells with n < min_co_tested are NA.

T_matrix

Integer matrix of co-tested isolate counts.

R_matrix

Integer matrix of co-resistant isolate counts.

classes

Character vector of class names (row/column order).

Details

Matrices are computed for all tested classes – no filtering by marginal resistance or GBD core list is applied here.

Examples

if (FALSE) { # \dontrun{
marg <- compute_marginal_resistance(amr_clean, ...)
co_res <- compute_pairwise_coresistance(marg)

# Prevalence matrix for K. pneumoniae
co_res[["Klebsiella pneumoniae"]]$prevalence

# Co-tested counts
co_res[["Klebsiella pneumoniae"]]$T_matrix
} # }