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Check and Clean Composition Data

Source: R/5-rearrange_data.R
check_composition_data.Rd

This function checks the composition data for zero sum rows, handles NA values, and verifies that the composition data spans the required range of ages/lengths.

Usage

check_composition_data(data_list)

Arguments

data_list

A list containing the following components:

  • comp_obs: A matrix or data frame of composition observations.

  • comp_data: A data frame with metadata including species, sex, and age/length information.

  • nsex: A vector of sex counts by species.

  • nages: A vector of age counts by species.

  • nlengths: A vector of length counts by species. throws An error if any rows of comp_obs sum to 0 or if the composition data does not span the range of ages/lengths.

Value

The modified data_list with NA values in comp_obs converted to 0.

Examples

data_list <- list(
  comp_obs = matrix(c(1, 2, 3, 4, 5, 6), nrow = 2),
  comp_data = data.frame(Species = c(1, 2), Sex = c(1, 1), Age0_Length1 = c(0, 0)),
  nsex = c(1, 1),
  nages = c(3, 3),
  nlengths = c(3, 3)
)
cleaned_data_list <- check_composition_data(data_list)