Dataset curation for phylogenetically aware regression — phyloaware_dataset

Curate three datasetes for phylogenetically aware regression.

Usage

phyloaware_dataset_curation(
  trait,
  df,
  first_present = FALSE,
  patient_id = NULL,
  culture_date = NULL
)

Arguments

trait: Outcome of interest. Character string.
df: Dataset with trait variable and asr_cluster. Must contain patient_id and culture_date variables if first_present == TRUE.
first_present: Boolean (i.e., TRUE/FALSE) indicating whether to take the first present isolate
patient_id: Variable that contains IDs that group tips (i.e., Patient ID). Character string.
culture_date: Variable that contains collection/culture date. Character string. Variable must be formatted as a date.

Value

Three datasets labeled as 'present', 'singleton', and 'cluster'.

Details

Datasets included: 1. Present: All isolates 2. Singleton: Singleton isolates-only 3. Cluster: Cluster isolates-only

This permits isolated analysis of singleton and cluster isolates, enabling identification of characteristics associated with the emergence and/or spread of a trait.