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Compute Dietary Species Richness (DSR)

Source: R/compute_dsr.R
compute_dsr.Rd

Computes the Dietary Species Richness (DSR) score from cleaned dietary recall data. The function counts the number of distinct species consumed per respondent or recall ID. Users can either use the package FCT database (online CSV) or supply their own mapping file.

Usage

compute_dsr(
  recall_data,
  id_col,
  food_item_col,
  use_fct_db = FALSE,
  dsr_map_data = NULL,
  dsr_map_food = NULL,
  dsr_map_col = NULL,
  add_prefix = NULL
)

Arguments

recall_data

A data frame containing at least the ID column and the food item column.

id_col

Character. Name of the identifier column in recall_data (e.g., "survey_id").

food_item_col

Character. Column in recall_data containing food item names.

use_fct_db

Logical, default = FALSE. If TRUE, uses the package's online FCT database (species column).

dsr_map_data

Optional. A user-provided mapping data frame with food items and species names. Required if use_fct_db = FALSE.

dsr_map_food

Character. Column name in dsr_map_data that matches food items.

dsr_map_col

Character. Column name in dsr_map_data containing species names.

add_prefix

Optional character. Prefix to add to the output column name (e.g., "child" will produce child_dsr).

Value

A tibble with:

  • The ID column (as provided in id_col)

  • One column for the computed dietary species richness (dsr or prefixed name)

Details

  • If use_fct_db = TRUE, the function pulls from the online FCT database used in dietrecallkitR.

  • Foods with "No Species Assignment" or NA species are excluded from the count.

  • Duplicate species per ID are counted once.

  • Returns warnings for unmapped items.

Examples

# Using online FCT DB
recall_sample <- data.frame(
  survey_id = c(1, 1, 2, 2, 3),
  desc_of_food = c(
    "Rabbit meat, raw",
    "Ghee (cow milk)",
    "Cheese, cheddar, regular fat",
    "Tuna, grilled",
    "Rabbit meat, raw"
  )
)

result <- compute_dsr(
  recall_data   = recall_sample,
  id_col        = "survey_id",
  food_item_col = "desc_of_food",
  use_fct_db    = TRUE
)
print(result)
#> # A tibble: 3 × 2
#>   survey_id   dsr
#>       <dbl> <int>
#> 1         1     2
#> 2         2     2
#> 3         3     1

# Using custom mapping
species_map <- data.frame(
  item = c("Rabbit meat, raw", "Tuna, grilled", "Cheese, cheddar, regular fat", "Ghee (cow milk)"),
  species = c("Rabbit", "Tuna", "Cow", "Cow")
)

result <- compute_dsr(
  recall_data   = recall_sample,
  id_col        = "survey_id",
  food_item_col = "desc_of_food",
  use_fct_db    = FALSE,
  dsr_map_data  = species_map,
  dsr_map_food  = "item",
  dsr_map_col   = "species",
  add_prefix    = "child"
)
print(result)
#> # A tibble: 3 × 2
#>   survey_id child_dsr
#>       <dbl>     <int>
#> 1         1         2
#> 2         2         2
#> 3         3         1