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Calculate Deaths by Infectious Syndrome (D_L)

Source: R/burden.R
calculate_syndrome_deaths.Rd

Computes D_L, the number of deaths due to each infectious syndrome L.

Usage

calculate_syndrome_deaths(
  d_j = NULL,
  s_j = NULL,
  m_lj = NULL,
  pop_data = NULL,
  facility_data = NULL,
  cause_col = "cause_of_death",
  syndrome_col = "syndrome",
  syndrome = NULL,
  deaths_col = NULL,
  infection_flag_col = "is_infection_death",
  outcome_col = "final_outcome",
  death_value = "Died",
  patient_col = "patient_id",
  facility_col = NULL,
  facility_name = NULL,
  groupby_cols = NULL
)

Arguments

d_j

Data frame. Output of calculate_deaths_by_cause(). Supply together with s_j and m_lj for Mode 1. Default NULL.

s_j

Data frame. Output of calculate_infection_fraction(). Default NULL.

m_lj

Data frame. Output of calculate_syndrome_fraction(). Default NULL.

pop_data

Data frame. Raw population-level data for Mode 2. Default NULL.

facility_data

Data frame. Facility-level data for Mode 3 fallback. Default NULL.

cause_col

Character. Underlying cause column used in Modes 1 and 2. Default "cause_of_death".

syndrome_col

Character. Column containing syndrome labels in both population and facility data. Default "syndrome".

syndrome

Character. Optional. Name of a specific syndrome to filter results to (e.g., "Bloodstream infection"). NULL returns all syndromes. Default NULL.

deaths_col

Character. Pre-aggregated deaths column in pop_data (Mode 2 only). NULL means each row is one death record. Default NULL.

infection_flag_col

Character. Binary infection flag column in pop_data (Modes 1 and 2). Default "is_infection_death".

outcome_col

Character. Outcome column in facility_data (Mode 3). Default "final_outcome".

death_value

Character. Value in outcome_col that represents death. Accepts any string, e.g., "Died" or "Death". Default "Died".

patient_col

Character. Unique patient identifier column in facility_data. Deaths are counted as distinct patients, not rows. Default "patient_id".

facility_col

Character. Column containing facility names in facility_data. Required when facility_name is specified. Default NULL.

facility_name

Character. Name of a specific facility to restrict the analysis to. NULL uses all facilities combined. Default NULL.

groupby_cols

Character vector. Additional stratification columns (e.g., c("Age_bin", "gender")). Default NULL.

Value

Data frame with columns: syndrome_col, any groupby_cols, D_L (deaths by syndrome), D_L_method, D_L_confidence.

Details

Three operating modes, evaluated in priority order:

  1. Pre-computed components (HIGH confidence): pass the outputs of calculate_deaths_by_cause(), calculate_infection_fraction(), and calculate_syndrome_fraction() via d_j, s_j, and m_lj. Computes: D_L = sum_J(D_J * S_J * M_LJ).

  2. Raw population data (HIGH confidence): pass pop_data and all three components are computed internally before combining. Computes: D_L = sum_J(D_J * S_J * M_LJ).

  3. Facility fallback (LOW confidence): when no population inputs are available, counts the number of unique patients who died for each syndrome directly from facility_data.

Use syndrome to restrict results to a single syndrome of interest. Use facility_col and facility_name to restrict the facility fallback to a specific site.

References

Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019. Lancet. 2022.

Examples

if (FALSE) { # \dontrun{
# Mode 1: pass pre-computed components, all syndromes
d_j <- calculate_deaths_by_cause(pop_data = vr, cause_col = "icd10")
s_j <- calculate_infection_fraction(pop_data = vr, cause_col = "icd10")
m_lj <- calculate_syndrome_fraction(
  pop_data = vr, cause_col = "icd10", syndrome_col = "syndrome"
)
d_l <- calculate_syndrome_deaths(
  d_j = d_j, s_j = s_j, m_lj = m_lj,
  cause_col = "icd10", syndrome_col = "syndrome"
)

# Mode 2: raw population data, filter to one syndrome
d_l <- calculate_syndrome_deaths(
  pop_data     = vital_reg,
  cause_col    = "icd10_cause",
  syndrome_col = "infectious_syndrome",
  syndrome     = "Bloodstream infection"
)

# Mode 3: facility fallback, one facility, all syndromes
d_l <- calculate_syndrome_deaths(
  facility_data = amr_data,
  syndrome_col  = "specimen_normalized",
  outcome_col   = "final_outcome",
  death_value   = "Died",
  patient_col   = "patient_id",
  facility_col  = "location",
  facility_name = "Mumbai"
)

# Mode 3: facility fallback, all facilities, one syndrome, stratified by age
d_l <- calculate_syndrome_deaths(
  facility_data = amr_data,
  syndrome_col  = "specimen_normalized",
  syndrome      = "Blood",
  death_value   = "Died",
  groupby_cols  = c("Age_bin")
)
} # }