[R] Best way to test for numeric digits?

Wed Oct 18 19:19:28 CEST 2023

Rui,

The problem with searching for elements, as with many kinds of text, is that the optimal search order may depend on the probabilities of what is involved. There can be more elements added such as Unobtainium in the future with whatever abbreviations that may then change the algorithm you may have chosen but then again, who actually looks for elements with a negligible half-life?

If you had an application focused on Organic Chemistry, a relatively few of the elements would normally be present while for something like electronics components of some kind, a different overlapping palette with probabilities can be found.

Just how important is the efficiency for you? If this was in a language like python, I would consider using a dictionary or set and I think there are packages in R that support a version of this.  In your case, one solution can be to pre-create a dictionary of all the elements, or just a set, and take your word tokens and check if they are in the dictionary/set or not. Any that aren't can then be further examined as needed and if your data is set a specific way, they may all just end up to be numeric. The cost is the hashing and of course memory used. Your corpus of elements is small enough that this may not be as helpful as parsing text that can contain many thousands of words.

Even in plain R, you can probably also use something like:

elements = c("H", "He", "Li", ...)
If (text %in% elements) ...

Something like the above may not be faster but can be quite a bit more readable than the regular expressions

But plenty of the solutions others offered may well be great for your current need.

Some may even work with Handwavium.

-----Original Message-----
From: R-help <r-help-bounces using r-project.org> On Behalf Of Leonard Mada via R-help
Sent: Wednesday, October 18, 2023 12:24 PM
To: Rui Barradas <ruipbarradas using sapo.pt>; R-help Mailing List <r-help using r-project.org>
Subject: Re: [R] Best way to test for numeric digits?

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
>
>

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