Format Data for Because Analysis

Converts data from long format (one row per observation) to the list format required by because.

Usage

because_format_data(data, species_col = "SP", tree = NULL)

Arguments

data

A data.frame in long format with one row per observation.

species_col

Name of the column containing species or unit identifiers (default: "SP").

tree

A phylogenetic tree or other structural object. Optional. If provided, determines the order of units.

Value

A named list where each element is either:

• A numeric vector (if all species have exactly 1 observation)

• A numeric matrix with species in rows and replicates in columns

Species are ordered to match tree$tip.label (if provided) or sorted alphabetically.

Details

This function handles:

• Different numbers of replicates per species (creates rectangular matrix with NA padding)

• Missing values (NA)

• Automatic alignment with phylogenetic tree tip labels (if provided)

When species have different numbers of replicates, the function creates a matrix with dimensions (number of species) x (maximum number of replicates). Species with fewer replicates are padded with NA values.

If a tree is provided: Species in the tree but not in the data will have all NA values. Species in the data but not in the tree will be excluded with a warning.

If no tree is provided: All species in the data are included, sorted alphabetically by their ID.

Examples

if (FALSE) { # \dontrun{
# Example data in long format
data_long <- data.frame(
  SP = c("sp1", "sp1", "sp1", "sp2", "sp2", "sp3"),
  BM = c(1.2, 1.3, 1.1, 2.1, 2.2, 1.8),
  NL = c(0.5, 0.6, NA, 0.7, 0.8, 0.9)
)

# With tree
if (requireNamespace("ape", quietly = TRUE)) {
  tree <- ape::read.tree(text = "(sp1:1,sp2:1,sp3:1);")
  data_list <- because_format_data(data_long, species_col = "SP", tree = tree)
}

# Without tree (general repeated measures)
data_list_no_tree <- because_format_data(data_long, species_col = "SP")
} # }