Validate user inputs to instar_report()

Checks that the items table is well-formed, that every item_id it references exists in instar_items, and that any status column uses the canonical levels. Returns the table in canonical form, with status derived from value if it was absent.

Usage

validate_items(items, items_ref = instar_items, strict = TRUE)

Arguments

items

A data frame with at least item_id and value columns.

items_ref

The framework to validate against. Defaults to instar_items.

strict

Logical. If TRUE (the default), unknown item_ids raise an error. If FALSE, they are warned about and dropped.

Value

The validated items table, with the instar_items class and a canonical status column. Errors if validation fails.

Examples

tmpl <- instar_template()
validate_items(tmpl)
#> 
#>   Subjects
#>     o  Taxonomic ID, life stage, & sex
#>     o  Source & culture history
#>     o  Sample size & attrition
#> 
#>   Procedures
#>     o  Capture, transport, & handling
#>     o  Anaesthesia, analgesia, & invasive procedures
#>     o  Containment & biosecurity
#> 
#>   Ethics & Compliance
#>     o  Ethics review, permits, & conservation status
#>     o  Humane endpoints & non-target impacts
#>     o  Welfare & 3Rs statement
#> 
#>   Nutrition
#>     o  Diet, feeding, & water
#> 
#>   Environment
#>     o  Housing & abiotic conditions
#>     o  Acclimation
#>     o  Field site & collection
#> 
#>   Health
#>     o  Health monitoring
#>     o  Injury & mortality
#>     o  End of study
#> 
#>   Behaviour
#>     o  Behavioural opportunities, enrichment, & disturbance
#> 
#>   Affective state
#>     o  Indicators & precautionary measures
#>