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Calculate YLD per pathogen

Source: R/burden.R
calculate_YLD.Rd

Computes Years Lived with Disability (YLD) attributable to each pathogen K within syndrome L:

Usage

calculate_YLD(
  incidence_data,
  P_Lk_prime_tbl,
  yld_ref = NULL,
  DW_sepsis = NULL,
  avg_los_years = NULL,
  state_name = NULL,
  facility_col = NULL,
  facility_name = NULL,
  facility_state_map = NULL,
  state_col = "state",
  pathogen_col = "pathogen",
  pathogen_name = NULL,
  plk_col = "P_Lk_prime",
  incidence_col = "n_cases"
)

Arguments

incidence_data

Numeric scalar (pooled) or data frame with facility_col + incidence_col columns (facility-level).

P_Lk_prime_tbl

Data frame from calculate_P_Lk_prime(). Use the P_Lk_prime element for pooled mode or the facility_level element for facility-level mode.

yld_ref

Data frame with columns location_name and DW_sepsis. Loaded from inst/extdata/Proxy_YLD_per_case.xlsx. Optional if DW_sepsis is provided.

DW_sepsis

Numeric scalar or NULL. If provided, this value is used directly for all rows and yld_ref is ignored.

avg_los_years

Numeric scalar or NULL. Overall average length of stay in years across all patients (resistant and susceptible combined), used to convert DW to a duration-weighted value: effective_DW = DW_sepsis * avg_los_years. If NULL, DW_sepsis is used as-is (caller is responsible for duration weighting).

state_name

Character or NULL. State for YLD weight in pooled mode. NULL uses the India row. Ignored in facility-level mode when DW_sepsis is provided.

facility_col

Character or NULL. Facility identifier column.

facility_name

Character or NULL. Restrict to one facility only.

facility_state_map

Data frame with facility_col and state_col columns, mapping each facility to its state. Required in facility-level mode only when DW_sepsis is not provided.

state_col

Character. Column in facility_state_map containing state names that match yld_ref$location_name. Default "state".

pathogen_col

Character. Pathogen column in P_Lk_prime_tbl. Default "pathogen".

pathogen_name

Character vector or NULL. If provided, restricts output to those pathogen(s) only.

plk_col

Character. P'LK column in P_Lk_prime_tbl. Default "P_Lk_prime".

incidence_col

Character. Incidence column when incidence_data is a data frame. Default "n_cases".

Value

Data frame with columns: pathogen_col, P_Lk_prime, incidence_L, DW_sepsis, YLD, and facility_col / state_col when in facility-level mode.

Details

$$YLD_K = \text{Incidence}_L \times P'_{LK} \times \text{DW\_sepsis}$$

The YLD weight per incident case is drawn from a GBD-derived reference table stratified by Indian state (yld_ref) when DW_sepsis is not provided. If DW_sepsis is provided directly, that scalar is used for all rows and yld_ref is ignored.

Facility-level mode (when facility_col is supplied and facility_name is NULL): P_Lk_prime_tbl must contain a facility_col column (i.e., the facility_level element from calculate_P_Lk_prime()). incidence_data must be a data frame with facility_col and an incidence count column. A facility_state_map data frame linking each facility to its state is required only when DW_sepsis is not supplied.

Pooled / no-facility mode: incidence_data is a single numeric scalar and P_Lk_prime_tbl has no facility column. state_name selects the YLD weight; defaults to "India" if NULL.