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Values represented by ECOTOX character to numeric

Source: R/process.r
as_numeric_ecotox.Rd

[Experimental] 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)

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.

Value

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

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.

Author

Pepijn de Vries

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)
#>  [1]   10.000    2.000    3.000    5.000    9.200    2.330 2333.000    2.100
#>  [9]       NA    0.001
#> attr(,"has_notation")
#>  [1] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE
#> attr(,"has_brackets")
#>  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE

## Text fields reported as ranges are processed with `range_fun`
as_numeric_ecotox(char_num, range_fun = median)
#>  [1]   10.000    2.000    3.000    5.000    9.200    2.330 2333.000    2.100
#>  [9]    3.000    0.001
#> attr(,"has_notation")
#>  [1] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE
#> attr(,"has_brackets")
#>  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE