Best way to test for numeric digits?

Wed, Oct 18, 2023 10:45 AM

?s 17:24 de 18/10/2023, Leonard Mada escreveu:

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:

?s 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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Hello,

You and Avi are right, my function's performance is terrible. The 
following is much faster.

As for how to not have digits throw warnings, the lapply in the version 
of your function below solves it by setting grep argument invert = TRUE. 
This will get all strings where digits do not occur.



split_chem_elements <- function(x, rm.digits = TRUE) {
   regex <- "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[A-Z])|(?<=[a-z])(?=[^a-z])"
   if(rm.digits) {
     stringr::str_replace_all(mol, regex, "#") |>
       strsplit("#|[[:digit:]]") |>
       lapply(\(x) x[nchar(x) > 0L])
   } else {
     strsplit(x, regex, perl = TRUE)
   }
}

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])"
   s <- strsplit(x, regex, perl = TRUE)
   if(rm.digits) {
     s <- lapply(s, \(x) x[grep("[[:digit:]]+", x, invert = TRUE)])
   }
   s
}

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"
split.symbol.character(mol)
#> [[1]]
#> [1] "C"  "Cl" "F"
#>
#> [[2]]
#> [1] "Li" "Al" "H"
#>
#> [[3]]
#>  [1] "C"  "Cl" "C"  "O"  "Al" "P"  "O"  "Si" "O"  "Cl"

mol10000 <- rep(mol, 10000)

system.time(
   split_chem_elements(mol10000)
)
#>    user  system elapsed
#>    0.01    0.00    0.02
system.time(
   split.symbol.character(mol10000)
)
#>    user  system elapsed
#>    0.35    0.07    0.47



Hope this helps,

Rui Barradas

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Best way to test for numeric digits?

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