List acceptable variable types for tags

This function returns a named list providing the acceptable data types for the default tags. If no argument is provided, it returns default values. Otherwise, provided values will be used to define the defaults.

Usage

tags_types(..., allow_extra = FALSE)

Arguments

...

a series of tags provided as tag_name = "column_name", where tag_name indicates any of the known variables listed in 'Details'; alternatively, a named list of variables to be tagged, where names indicate the types of variable (to be selected from tags_names()), and values indicate their name in the input data.frame; see details for a list of known variable types and their expected content

allow_extra

a logical indicating if additional data tags not currently recognized by linelist should be allowed; if FALSE, unknown tags will trigger an error

Value

A named list.

See also

• tags_defaults() for the default tags

• validate_types() uses tags_types() for validating tags

• validate_linelist() uses tags_types() for validating tags

Author

Thibaut Jombart thibaut@data.org

Examples

# list default values
tags_types()
#> $id
#> [1] "numeric"   "integer"   "character"
#> 
#> $date_onset
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_reporting
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_admission
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_discharge
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_outcome
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_death
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $gender
#> [1] "character" "factor"   
#> 
#> $age
#> [1] "numeric" "integer"
#> 
#> $location
#> [1] "character" "factor"   
#> 
#> $occupation
#> [1] "character" "factor"   
#> 
#> $hcw
#> [1] "logical"   "integer"   "character" "factor"   
#> 
#> $outcome
#> [1] "character" "factor"   
#> 

# change existing values
tags_types(date_onset = "Date") # impose a Date class
#> $id
#> [1] "numeric"   "integer"   "character"
#> 
#> $date_onset
#> [1] "Date"
#> 
#> $date_reporting
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_admission
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_discharge
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_outcome
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_death
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $gender
#> [1] "character" "factor"   
#> 
#> $age
#> [1] "numeric" "integer"
#> 
#> $location
#> [1] "character" "factor"   
#> 
#> $occupation
#> [1] "character" "factor"   
#> 
#> $hcw
#> [1] "logical"   "integer"   "character" "factor"   
#> 
#> $outcome
#> [1] "character" "factor"   
#> 

# add new types e.g. to allow genetic sequences using ape's format
tags_types(sequence = "DNAbin", allow_extra = TRUE)
#> $id
#> [1] "numeric"   "integer"   "character"
#> 
#> $date_onset
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_reporting
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_admission
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_discharge
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_outcome
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $date_death
#> [1] "integer" "numeric" "Date"    "POSIXct" "POSIXlt"
#> 
#> $gender
#> [1] "character" "factor"   
#> 
#> $age
#> [1] "numeric" "integer"
#> 
#> $location
#> [1] "character" "factor"   
#> 
#> $occupation
#> [1] "character" "factor"   
#> 
#> $hcw
#> [1] "logical"   "integer"   "character" "factor"   
#> 
#> $outcome
#> [1] "character" "factor"   
#> 
#> $sequence
#> [1] "DNAbin"
#>