[R] Best way to test for numeric digits?

[Leonard Mada]

Dear Rui,

Thank you for your reply.

I do have actually access to the chemical symbols: I have started to 
refactor and enhance the Rpdb package, see Rpdb::elements:
https://github.com/discoleo/Rpdb

However, the regex that you have constructed is quite heavy, as it needs 
to iterate through all chemical symbols (in decreasing nchar). Elements 
like C, and especially O, P or S, appear late in the regex expression - 
but are quite common in chemistry.

The alternative regex is (in this respect) simpler. It actually works 
(once you know about the workaround).

Q: My question focused if there is anything like is.numeric, but to 
parse each element of a vector.

Sincerely,


Leonard


On 10/18/2023 6:53 PM, Rui Barradas wrote:
> Às 15:59 de 18/10/2023, Leonard Mada via R-help escreveu:
>> Dear List members,
>>
>> What is the best way to test for numeric digits?
>>
>> suppressWarnings(as.double(c("Li", "Na", "K",  "2", "Rb", "Ca", "3")))
>> # [1] NA NA NA  2 NA NA  3
>> The above requires the use of the suppressWarnings function. Are there
>> any better ways?
>>
>> I was working to extract chemical elements from a formula, something
>> like this:
>> split.symbol.character = function(x, rm.digits = TRUE) {
>>       # Perl is partly broken in R 4.3, but this works:
>>       regex = "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
>>       # stringi::stri_split(x, regex = regex);
>>       s = strsplit(x, regex, perl = TRUE);
>>       if(rm.digits) {
>>           s = lapply(s, function(s) {
>>               isNotD = is.na(suppressWarnings(as.numeric(s)));
>>               s = s[isNotD];
>>           });
>>       }
>>       return(s);
>> }
>>
>> split.symbol.character(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"))
>>
>>
>> Sincerely,
>>
>>
>> Leonard
>>
>>
>> Note:
>> # works:
>> regex = "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
>> strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl = T)
>>
>>
>> # broken in R 4.3.1
>> # only slightly "erroneous" with stringi::stri_split
>> regex = "(?<=[A-Z])(?![a-z]|$)|(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
>> strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl = T)
>>
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>> and provide commented, minimal, self-contained, reproducible code.
> Hello,
>
> If you want to extract chemical elements symbols, the following might work.
> It uses the periodic table in GitHub package chemr and a package stringr
> function.
>
>
> devtools::install_github("paleolimbot/chemr")
>
>
>
> split_chem_elements <- function(x) {
>     data(pt, package = "chemr", envir = environment())
>     el <- pt$symbol[order(nchar(pt$symbol), decreasing = TRUE)]
>     pat <- paste(el, collapse = "|")
>     stringr::str_extract_all(x, pat)
> }
>
> mol <- c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl")
> split_chem_elements(mol)
> #> [[1]]
> #> [1] "C"  "Cl" "F"
> #>
> #> [[2]]
> #> [1] "Li" "Al" "H"
> #>
> #> [[3]]
> #>  [1] "C"  "Cl" "C"  "O"  "Al" "P"  "O"  "Si" "O"  "Cl"
>
>
> It is also possible to rewrite the function without calls to non base
> packages but that will take some more work.
>
> Hope this helps,
>
> Rui Barradas
>
>