Re: [R] Best way to test for numeric digits?
Leonard,
Since it now seems a main consideration you have is speed/efficiency, maybe a
step back might help.
Are there simplifying assumptions that are valid or can you make it simpler,
such as converting everything to the same case?
Your sample data was this and I assume your actual data is similar and far
longer.
c("Li", "Na", "K", "2", "Rb", "Ca", "3")
So rather than use complex and costly regular expressions, or other full
searches, can you just assume all entries start with either an uppercase letter
orn a numeral and test for those usinnd something simple like
> substr(c("Li", "Na", "K", "2", "Rb", "Ca", "3"), 1, 1)
[1] "L" "N" "K" "2" "R" "C" "3"
If you save that in a variable you can check if that is greater than or equal
to "A" or perhaps "0" and also perhaps if it is less than or equal to "Z" or
perhaps "9" and see if such a test is faster.
orig <- c("Li", "Na", "K", "2", "Rb", "Ca", "3")
initial <- substr(orig, 1, 1)
elements_bool <- initial >= "A" & initial <= "Z"
The latter contains a Boolean vector you can use to index your original and
toss away the ones with digits, or any lower case letter versions or any other
UNICODE symbols.
orig_elements <- orig[elements_bool]
> orig
[1] "Li" "Na" "K" "2" "Rb" "Ca" "3"
> orig_elements
[1] "Li" "Na" "K" "Rb" "Ca"
> orig[!elements_bool]
[1] "2" "3"
Other approaches you might consider depending on your needs is to encapsulate
your data as a column in a data.frame or tibble or other such construct and
generate additional columns along the way that keep your information
consolidated in what could be an efficient way especially if you shift some of
your logic to using faster compiled functionality and perhaps using packages
that fit your needs better such as data.table or dplyr and other things in the
tidyverse. And note if using pipelines, for many purposes, the new built-in
pipelines may be faster.
-Original Message-
From: R-help On Behalf Of Leonard Mada via R-help
Sent: Wednesday, October 18, 2023 10:59 AM
To: R-help Mailing List
Subject: [R] Best way to test for numeric digits?
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)
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
This seems unnecessarily complex. Or rather,
it pushes the complexity into an arcane notation
What we really want is something that says "here is a string,
here is a pattern, give me all the substrings that match."
What we're given is a function that tells us where those
substrings are.
# greg.matches(pattern, text)
# accepts a POSIX regular expression, pattern
# and a text to search in. Both arguments must be character strings
# (length(...) = 1) not longer vectors of strings.
# It returns a character vector of all the (non-overlapping)
# substrings of text as determined by gregexpr.
greg.matches <- function (pattern, text) {
if (length(pattern) > 1) stop("pattern has too many elements")
if (length(text)> 1) stop( "text has too many elements")
match.info <- gregexpr(pattern, text)
starts <- match.info[[1]]
stops <- attr(starts, "match.length") - 1 + starts
sapply(seq(along=starts), function (i) {
substr(text, starts[i], stops[i])
})
}
Given greg.matches, we can do the rest with very simple
and easily comprehended regular expressions.
# parse.chemical(formula)
# takes a simple chemical formula "..." and
# returns a list with components
# $elements -- character -- the atom symbols
# $counts -- number-- the counts (missing counts taken as 1).
# BEWARE. This does not handle formulas like "CH(OH)3".
parse.chemical <- function (formula) {
parts <- greg.matches("[A-Z][a-z]*[0-9]*", formula)
elements <- gsub("[0-9]+", "", parts)
counts <- as.numeric(gsub("[^0-9]+", "", parts))
counts <- ifelse(is.na(counts), 1, counts)
list(elements=elements, counts=counts)
}
> parse.chemical("CCl3F")
$elements
[1] "C" "Cl" "F"
$counts
[1] 1 3 1
> parse.chemical("Li4Al4H16")
$elements
[1] "Li" "Al" "H"
$counts
[1] 4 4 16
> parse.chemical("CCl2CO2AlPO4SiO4Cl")
$elements
[1] "C" "Cl" "C" "O" "Al" "P" "O" "Si" "O" "Cl"
$counts
[1] 1 2 1 2 1 1 4 1 4 1
On Thu, 19 Oct 2023 at 03:59, Leonard Mada via R-help
wrote:
> Dear List members,
>
> What is the best way to test for numeric digits?
>
> suppressWarnings(as.double(c("Li", "Na", "K", "2", "Rb", "Ca", "3")))
> # [1] NA NA NA 2 NA NA 3
> The above requires the use of the suppressWarnings function. Are there
> any better ways?
>
> I was working to extract chemical elements from a formula, something
> like this:
> split.symbol.character = function(x, rm.digits = TRUE) {
> # Perl is partly broken in R 4.3, but this works:
> regex = "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[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)
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
Please delete drjimle...@bitwrit.com from your mailing list. He passed away
a month ago.
Regards,
Juel (wife)
On Thu, 19 Oct 2023, 02:09 Ben Bolker There are some answers on Stack Overflow:
>
>
> https://stackoverflow.com/questions/14984989/how-to-avoid-warning-when-introducing-nas-by-coercion
>
>
>
> On 2023-10-18 10:59 a.m., Leonard Mada via R-help wrote:
> > 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)
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
The matching approach is also competitive:
match.symbol2 <- function(x, rm.digits = TRUE) {
if (rm.digits) stringi::stri_extract_all(x, regex = '[A-Z][a-z]*') else
lapply(
stringi::stri_match_all(x, regex = '([A-Z][a-z]*)([0-9]*)'), \(m) {
m <- t(m[,2:3]); m[nzchar(m)]
}
)
}
mol5 <- rep(mol, 5)
system.time(split.symbol.character(mol5))
# user system elapsed
# 1.518 0.000 1.518
system.time(split_chem_elements(mol5))
# user system elapsed
# 0.435 0.000 0.436
system.time(match.symbol2(mol5))
# user system elapsed
# 0.117 0.000 0.117
--
Best regards,
Ivan
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
Às 19:35 de 18/10/2023, Leonard Mada escreveu:
Dear Rui,
On 10/18/2023 8:45 PM, Rui Barradas wrote:
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
}
You have a glitch (mol is hardcoded) in the code of the first function.
The times are similar, after correcting for that glitch.
Note:
- grep("[[:digit:]]", ...) behaves almost twice as slow as grep("[0-9]",
...)!
- corrected results below;
Sincerely,
Leonard
###
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(x, 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("[0-9]", x, invert = TRUE)])
}
s
}
mol <- c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl")
mol1 <- rep(mol, 1)
system.time(
split_chem_elements(mol1)
)
# user system elapsed
# 0.58 0.00 0.58
system.time(
split.symbol.character(mol1)
)
# user system elapsed
# 0.67 0.00 0.67
Hello,
You are right, sorry for the blunder :(.
In the code below I have replaced stringr::str_replace_all by the
package stringi function stri_replace_all_regex and the improvement is
significant.
split_chem_elements <- function(x, rm.digits = TRUE) {
regex <- "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[A-Z])|(?<=[a-z])(?=[^a-z])"
if(rm.digits) {
stringi::stri_replace_all_regex(x, "#", regex) |>
strsplit("#|[0-9]") |>
lapply(\(x) x[nchar(x) > 0L])
} else {
strsplit(x, regex, perl = TRUE)
}
}
# system.time(
# split_chem_elements(mol1)
# )
# user system elapsed
# 0.060.000.09
# system.time(
# split.symbol.character(mol1)
# )
# user system elapsed
# 0.250.000.28
Hope this helps,
Rui Barradas
--
Este e-mail foi analisado pelo software antivírus AVG para verificar a presença
de vírus.
www.avg.com
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
Dear Rui,
On 10/18/2023 8:45 PM, Rui Barradas wrote:
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
}
You have a glitch (mol is hardcoded) in the code of the first function.
The times are similar, after correcting for that glitch.
Note:
- grep("[[:digit:]]", ...) behaves almost twice as slow as grep("[0-9]",
...)!
- corrected results below;
Sincerely,
Leonard
###
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(x, 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("[0-9]", x, invert = TRUE)])
}
s
}
mol <- c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl")
mol1 <- rep(mol, 1)
system.time(
split_chem_elements(mol1)
)
# user system elapsed
# 0.58 0.00 0.58
system.time(
split.symbol.character(mol1)
)
# user system elapsed
# 0.67 0.00 0.67
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
Às 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:
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]|$)|(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl = T)
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://eu01.z.antigena.com/l/boS9jwics77ZHEe0yO-Lt8AIDZm9-s6afEH4ulMO3sMyE9mLHNAR603_eeHQG2-_t0N2KsFVQRcldL-XDy~dLMhLtJWX69QR9Y0E8BCSopItW8RqG76PPj7ejTkm7UOsLQcy9PUV0-uTjKs2zeC_oxUOrjaFUWIhk8xuDJWb
PLEASE do read the posting guide
https://eu01.z.antigena.com/l/rUSt2cEKjOO0HrIFcEgHH_NROfU9g5sZ8MaK28fnBl9G6CrCrrQyqd~_vNxLYzQ7Ruvlxfq~P_77QvT1BngSg~NLk7joNyC4dSEagQsiroWozpyhR~tbGOGCRg5cGlOszZLsmq2~w6qHO5T~8b5z8ZBTJkCZ8CBDi5KYD33-OK
and provide commented, minimal, self-contained, reproducible code.
Hello,
If you want to extract chemical elements symbols, the following might
work.
It uses the periodic table in GitHub package chemr and a package stringr
function.
devtools::install_github("paleolimbot/chemr")
split_chem_elements <- function(x) {
data(pt, package = "chemr", envir = environment())
el <- pt$symbol[order(nchar(pt$symbol), decreasing = TRUE)]
pat <- paste(el, collapse = "|")
stringr::str_extract_all(x, pat)
}
mol <- c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl")
split_chem_elements(mol)
#> [[1]]
#> [1] "C" "Cl" "F"
#>
#> [[2]]
#> [1] "Li" "Al" "H"
#>
#> [[3]]
#> [1] "C" "Cl" "C" "O" "Al" "P" "O" "Si" "O" "Cl"
It is also possible to rewrite the function without calls to non base
packages but that will take some more work.
Hope this helps,
Rui Barradas
Hello,
You and Avi are right, my function's performance is terrible. The
following is much faster.
As for how to not have digits throw warnings, the lapply in the version
of your function below solves it by setting grep argument invert = TRUE.
This will get all strings where digits do not occur.
split_chem_elements <- function(x, rm.digits = TRUE) {
regex <- "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[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"
mol1 <- rep(mol, 1)
system.time(
split_chem_elements(mol1)
)
#>user system elapsed
#>0.010.000.02
Re: [R] Best way to test for numeric digits?
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 On Behalf Of Leonard Mada via R-help
Sent: Wednesday, October 18, 2023 12:24 PM
To: Rui Barradas ; R-help Mailing List
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]|$)|(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
>> strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl = T)
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://eu01.z.antigena.com/l/boS9jwics77ZHEe0yO-Lt8AIDZm9-s6afEH4ulMO3sMyE9mLHNAR603_eeHQG2-_t0N2KsFVQRcldL-XDy~dLMhLtJWX69QR9Y0E8BCSopItW8RqG76PPj7ejTkm7UOsLQcy9PUV0-uTjKs2zeC_oxUOrjaFUWIhk8xuDJWb
>> PLEASE
Re: [R] Best way to test for numeric digits?
Dear Rui,
Thank you for your reply.
I do have actually access to the chemical symbols: I have started to
refactor and enhance the Rpdb package, see Rpdb::elements:
https://github.com/discoleo/Rpdb
However, the regex that you have constructed is quite heavy, as it needs
to iterate through all chemical symbols (in decreasing nchar). Elements
like C, and especially O, P or S, appear late in the regex expression -
but are quite common in chemistry.
The alternative regex is (in this respect) simpler. It actually works
(once you know about the workaround).
Q: My question focused if there is anything like is.numeric, but to
parse each element of a vector.
Sincerely,
Leonard
On 10/18/2023 6:53 PM, Rui Barradas wrote:
Às 15:59 de 18/10/2023, Leonard Mada via R-help escreveu:
Dear List members,
What is the best way to test for numeric digits?
suppressWarnings(as.double(c("Li", "Na", "K", "2", "Rb", "Ca", "3")))
# [1] NA NA NA 2 NA NA 3
The above requires the use of the suppressWarnings function. Are there
any better ways?
I was working to extract chemical elements from a formula, something
like this:
split.symbol.character = function(x, rm.digits = TRUE) {
# Perl is partly broken in R 4.3, but this works:
regex = "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[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)
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://eu01.z.antigena.com/l/boS9jwics77ZHEe0yO-Lt8AIDZm9-s6afEH4ulMO3sMyE9mLHNAR603_eeHQG2-_t0N2KsFVQRcldL-XDy~dLMhLtJWX69QR9Y0E8BCSopItW8RqG76PPj7ejTkm7UOsLQcy9PUV0-uTjKs2zeC_oxUOrjaFUWIhk8xuDJWb
PLEASE do read the posting guide
https://eu01.z.antigena.com/l/rUSt2cEKjOO0HrIFcEgHH_NROfU9g5sZ8MaK28fnBl9G6CrCrrQyqd~_vNxLYzQ7Ruvlxfq~P_77QvT1BngSg~NLk7joNyC4dSEagQsiroWozpyhR~tbGOGCRg5cGlOszZLsmq2~w6qHO5T~8b5z8ZBTJkCZ8CBDi5KYD33-OK
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
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
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]|$)|(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl = T)
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Hello,
If you want to extract chemical elements symbols, the following might work.
It uses the periodic table in GitHub package chemr and a package stringr
function.
devtools::install_github("paleolimbot/chemr")
split_chem_elements <- function(x) {
data(pt, package = "chemr", envir = environment())
el <- pt$symbol[order(nchar(pt$symbol), decreasing = TRUE)]
pat <- paste(el, collapse = "|")
stringr::str_extract_all(x, pat)
}
mol <- c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl")
split_chem_elements(mol)
#> [[1]]
#> [1] "C" "Cl" "F"
#>
#> [[2]]
#> [1] "Li" "Al" "H"
#>
#> [[3]]
#> [1] "C" "Cl" "C" "O" "Al" "P" "O" "Si" "O" "Cl"
It is also possible to rewrite the function without calls to non base
packages but that will take some more work.
Hope this helps,
Rui Barradas
--
Este e-mail foi analisado pelo software antivírus AVG para verificar a presença
de vírus.
www.avg.com
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
В Wed, 18 Oct 2023 17:59:01 +0300
Leonard Mada via R-help пишет:
> What is the best way to test for numeric digits?
>
> suppressWarnings(as.double(c("Li", "Na", "K", "2", "Rb", "Ca", "3")))
> # [1] NA NA NA 2 NA NA 3
> The above requires the use of the suppressWarnings function. Are
> there any better ways?
This test also has the downside of accepting things like "1.2" and
"+1e-100". Since you need digits only, why not use a regular expression
to test for '^[0-9]+$'?
> I was working to extract chemical elements from a formula, something
> like this:
> split.symbol.character(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"))
Perhaps the following function could be made to work in your cases?
function(x) regmatches(x, gregexec('([A-Z][a-z]*)([0-9]*)', x))
retval[2,] is the element and retval[3,] is the coefficient. Do you
need brackets? Charges? Non-stoichiometric compounds? (SMILES?)
> # broken in R 4.3.1
> # only slightly "erroneous" with stringi::stri_split
> regex = "(?<=[A-Z])(?![a-z]|$)|(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
> strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl =
> T)
strsplit() has special historical behaviour about empty matches:
https://bugs.r-project.org/show_bug.cgi?id=16745
It's unfortunate that it doesn't split on empty matches the way you
would intuitively expect it to, but changing the behaviour at this
point is hard. Even adding a flag may be complicated to implement. Do
you want such a flag?
--
Best regards,
Ivan
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
Use any occurrence of one or more digits as a separator?
s <- c( "CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl" )
strsplit( s, "\\d+" )
On October 18, 2023 7:59:01 AM PDT, Leonard Mada via R-help
wrote:
>Dear List members,
>
>What is the best way to test for numeric digits?
>
>suppressWarnings(as.double(c("Li", "Na", "K", "2", "Rb", "Ca", "3")))
># [1] NA NA NA 2 NA NA 3
>The above requires the use of the suppressWarnings function. Are there any
>better ways?
>
>I was working to extract chemical elements from a formula, something like this:
>split.symbol.character = function(x, rm.digits = TRUE) {
> # Perl is partly broken in R 4.3, but this works:
> regex = "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[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)
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
--
Sent from my phone. Please excuse my brevity.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best way to test for numeric digits?
There are some answers on Stack Overflow:
https://stackoverflow.com/questions/14984989/how-to-avoid-warning-when-introducing-nas-by-coercion
On 2023-10-18 10:59 a.m., Leonard Mada via R-help wrote:
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]|$)|(?=[A-Z])|(?<=[a-z])(?=[^a-z])";
strsplit(c("CCl3F", "Li4Al4H16", "CCl2CO2AlPO4SiO4Cl"), regex, perl = T)
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Best way to test for numeric digits?
Dear List members,
What is the best way to test for numeric digits?
suppressWarnings(as.double(c("Li", "Na", "K", "2", "Rb", "Ca", "3")))
# [1] NA NA NA 2 NA NA 3
The above requires the use of the suppressWarnings function. Are there
any better ways?
I was working to extract chemical elements from a formula, something
like this:
split.symbol.character = function(x, rm.digits = TRUE) {
# Perl is partly broken in R 4.3, but this works:
regex = "(?<=[A-Z])(?![a-z]|$)|(?<=.)(?=[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)
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
