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Calculate syndrome incidence from deaths, CFR, and CR_L (formula-based)

Source: R/burden.R
calculate_incidence_L.Rd

Estimates the number of incident cases of syndrome L using:

Usage

calculate_incidence_L(
  deaths_L,
  cfr_lk_tbl,
  P_Lk_prime_tbl,
  CR_L = 1,
  pathogen_col = "pathogen",
  cfr_col = "CFR_LK",
  plk_col = "P_Lk_prime",
  facility_col = NULL,
  deaths_col = "deaths"
)

Arguments

deaths_L

Numeric scalar (pooled mode) or data frame with a facility_col column and a deaths_col column (facility-level mode).

cfr_lk_tbl

Data frame with at minimum columns pathogen_col and cfr_col. Typically the cfr_table element from calculate_cfr_lk().

P_Lk_prime_tbl

Data frame with pathogen_col and plk_col. Use the P_Lk_prime (pooled) element from calculate_P_Lk_prime_BSI() or calculate_P_Lk_prime().

CR_L

Numeric scalar. CFR adjustment factor from calculate_CR_L(). Default 1 (no adjustment).

pathogen_col

Character. Pathogen column in both tables. Default "pathogen".

cfr_col

Character. CFR column in cfr_lk_tbl. Default "CFR_LK".

plk_col

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

facility_col

Character or NULL. Facility identifier. When provided, cfr_lk_tbl and P_Lk_prime_tbl must each contain facility_col, and deaths_L must be a data frame with facility_col + deaths_col.

deaths_col

Character. Column in deaths_L data frame containing death counts. Default "deaths". Ignored when deaths_L is a scalar.

Value

Data frame with columns deaths, CFR_L, CR_L, I_L (incident cases), and facility_col when applicable.

Details

$$I_L = \frac{D_L}{\text{CFR}_L \times \text{CR}_L}$$

where the syndrome-level CFR is the pathogen-weighted average:

$$\text{CFR}_L = \sum_k P'_{Lk} \times \text{CFR}_{Lk}$$

Use this when you have population- or facility-level death counts and want to back-calculate incidence. For a direct patient count from facility data, use count_incident_cases() instead.