ECOTOXr (version 1.2.1)

as_numeric_ecotox: Values represented by ECOTOX character to numeric

Description

Similar to as.numeric(), but it also performs some text sanitising before coercing text to numerics.

Usage

as_numeric_ecotox(x, range_fun = NULL, ..., warn = TRUE)

Value

A vector of numeric values with the same length as x.

Arguments

x

A vector of character strings. It expects fields as commonly returned from the ECOTOX database.

range_fun

Function to summarise range values. If NULL range values are returned as NA

...

Arguments passed to range_fun.

warn

If set to FALSE warnings while converting text to numerics are suppressed.

Author

Pepijn de Vries

Details

The following steps are performed to sanitise text before coercing it to numerics:

• Notes labelled with "x" or "\*" are removed.

• Operators (">", ">=", "<", "<=", "~", "=", "ca", "er") are removed.

• Text between brackets ("()") is removed (including the brackets)

• Comma's are considered to be a thousand separator when they are located at any fourth character (from the right) and removed. Comma's at any other location is assumed to be a decimal separator and is replaced by a period.

• If there is a hyphen present (not preceded by an ""e" or "E") it is probably representing a range of values. When range_fun is NULL it will result in a NA. Otherwise, the numbers are split at the hyphen and aggregated with range_fun

It is your own responsibility to check if the sanitising steps are appropriate for your analyses.

See Also

Other ecotox-sanitisers: as_date_ecotox(), as_unit_ecotox(), mixed_to_single_unit(), process_ecotox_dates(), process_ecotox_numerics(), process_ecotox_units()

Examples

## a vector of commonly used notations in the database to represent
## numeric values 
char_num <- c("10", " 2", "3 ", "~5", "9.2*", "2,33",
              "2,333", "2.1(1.0 - 3.2)", "1-5", "1e-3")

## Text fields reported as ranges are returned as `NA`:
as_numeric_ecotox(char_num, warn = FALSE)

## Text fields reported as ranges are processed with `range_fun`
as_numeric_ecotox(char_num, range_fun = median)