I am trying to use Sys.glob to open a file called "apcp_sfc_latlon_subset_19940101_20071231.nc". The following command works:
> Sys.glob(file.path("data/train", "apcp*"))
[1] "data/train/apcp_sfc_latlon_subset_19940101_20071231.nc"
But this command doesn't return anything. I'm don't know why it doesn't work.
> Sys.glob(file.path("data/train", "apcp", "*"))
character(0)
I want the "apcp" bit as it's own argument because I will be passing a variable instead of a hard coded string.
Thank you.
file.path("data/train", "apcp", "*") returns "data/train/apcp/*" whereas file.path("data/train", "apcp*") returns "data/train/apcp*".
Thus in the first case you are looking for files in the subdirectoy apcp, and in the (working) case you are looking for files which begin apcp within the data\train directory.
If you want to be able to pass the apcp component as a argument, using paste0 will work
starting <- "apcp"
file.path("data/train", paste0(starting, '*', collapse =''))
# "data/train/apcp*"
Related
I need help with passing an argument as a variable name in an R script from the terminal. I'll run the script as follows:
R < script.R --args "hello"
And, in the script there should be something like this:
args <- commandArgs(trailingOnly = TRUE)
assign(args[1],24)
save(args[1], file="output.RData")
But, I need to take the argument as the variable name. What I mean is the following: If I run the script with "numbers" argument, the variable name inside the script should be numbers.
assign(args[1], 24)
does the trick. But, inside the save function, args[1] does not work. How can I pass it as a variable name?
Does it work if you try
saveRDS(get(args[1]),file="output.rds")
?
You won't get a text file with the save function. If you want its text version you would need to use `dump". This would "work" despirte the extention. The file ois still an .Rdata file event without the extension:
arg=1
argname="reports"
assign(argname, arg)
reports
#[1] 1
save(reports, file="test.txt")
rm(reports)
rm(argname)
rm(arg)
load("test.txt")
To use dump:
dump('reports', file="test2.txt")
This would appear in that file. It should be parse-able (and readable to humans) R code:
reports <-
1
This is likely a stupid question but I have not found a work around (at least in anything I have searched for, though I might just not be using the right search parameters.)
I want to call an executable in Windows, and send a file to it (in this case a Blaise man file), the name of which is variable in my script.
So, for example, I have
x<-2
myfile<-c(paste("FileNumber",x,".man", sep="")
system("myapp.exe" myfile)
But I simply get
Error: unexpected symbol in "system("myapp.exe" myfile"
as if the command is not recognizing the object as myfile, instead taking "myfile" as literal text.
I tried using a paste function to create a whole line command, but that also did not work.
The system command will not concatenate the string and the myfile object together, you have to do it yourself.
So, try this instead:
x<-2
myfile<-c(paste("FileNumber",x,".man", sep=""))
cmd <- paste("myapp.exe", myfile)
system(cmd)
Or just:
x<-2
system(paste("myapp.exe", c(paste("FileNumber",x,".man", sep=""))))
In R, I'm wondering if it's possible to temporarily redirect the output of the console to a variable?
p.s. There are a few examples on the web on how to use sink() to redirect the output into a filename, but none that I could find showing how to redirect into a variable.
p.p.s. The reason this is useful, in practice, is that I need to print out a portion of the default console output from some of the built-in functions in R.
I believe results <- capture.output(...) is what you need (i.e. using the default file=NULL argument). sink(textConnection("results")); ...; sink() should work as well, but as ?capture.output says, capture.output() is:
Related to ‘sink’ in the same way that ‘with’ is related to ‘attach’.
... which suggests that capture.output() will generally be better since it is more contained (i.e. you don't have to remember to terminate the sink()).
If you want to send the output of multiple statements to a variable you can wrap them in curly brackets {}, but if the block is sufficiently complex it might be better to use sink() (or make your code more modular by wrapping it in functions).
For the record, it's indeed possible to store stdout in a variable with the help of a temorary connection without calling capture.output -- e.g. when you want to save both the results and stdout. Example:
Prepare the variable for the diverted R output:
> stdout <- vector('character')
> con <- textConnection('stdout', 'wr', local = TRUE)
Divert the output:
> sink(con)
Do some stuff:
> 1:10
End the diversion:
> sink()
Close the temporary connection:
> close(con)
Check results:
> stdout
[1] " [1] 1 2 3 4 5 6 7 8 9 10"
Using R, I am looking to create a QR code and embed it into an Excel spreadsheet (hundreds of codes and spreadsheets). The obvious way seems to be to create a QR code using the command line, and use the "system" command in R. Does anyone know how to pass R variables through the "system" command? Google is not too helpful as "system" is a bit generic, ?system does not contain any examples of this.
Note - I am actually using data matrices rather than QR codes, but using the term "data matrix" in an R question will lead to havoc, so let's talk QR codes instead. :-)
system("dmtxwrite my_r_variable -o image.png")
fails, as do the variants I have tried with "paste". Any suggestions gratefully received.
Let's say we have the variable x that we want to pass on to dmtxwrite, you can pass it on like:
x = 10
system(sprintf("dmtxwrite %s -o image.png", x))
or alternatively using paste:
system(paste("dmtxwrite", x, "-o image.png"))
but I prefer sprintf in this case.
Also making use of base::system2 may be worth considering as system2 provides args argument that can be used for that purpose. In your example:
my_r_variable <- "a"
system2(
'echo',
args = c(my_r_variable, '-o image.png')
)
would return:
a -o image.png
which is equivalent to running echo in the terminal. You may also want to redirect output to text files:
system2(
'echo',
args = c(my_r_variable, '-o image.png'),
stdout = 'stdout.txt',
stderr = 'stderr.txt'
)
How can I find how did I first declare a certain variable when I am a few hundred
lines down from where I first declared it. For example, I have declared the following:
a <- c(vectorA,vectorB,vectorC)
and now I want to see how I declared it. How can I do that?
Thanks.
You could try using the history command:
history(pattern = "a <-")
to try to find lines in your history where you assigned something to the variable a. I think this matches exactly, though, so you may have to watch out for spaces.
Indeed, if you type history at the command line, it doesn't appear to be doing anything fancier than saving the current history in a tempfile, loading it back in using readLines and then searching it using grep. It ought to be fairly simple to modify that function to include more functionality...for example, this modification will cause it to return the matching lines so you can store it in a variable:
myHistory <- function (max.show = 25, reverse = FALSE, pattern, ...)
{
file1 <- tempfile("Rrawhist")
savehistory(file1)
rawhist <- readLines(file1)
unlink(file1)
if (!missing(pattern))
rawhist <- unique(grep(pattern, rawhist, value = TRUE,
...))
nlines <- length(rawhist)
if (nlines) {
inds <- max(1, nlines - max.show):nlines
if (reverse)
inds <- rev(inds)
}
else inds <- integer()
#file2 <- tempfile("hist")
#writeLines(rawhist[inds], file2)
#file.show(file2, title = "R History", delete.file = TRUE)
rawhist[inds]
}
I will assume you're using the default R console. If you're on Windows, you can File -> Save history and open the file in your fav text browser, or you can use function savehistory() (see help(savehistory)).
What you need to do is get a (good) IDE, or at least a decent text editor. You will benevit from code folding, syntax coloring and much more. There's a plethora of choices, from Tinn-R, VIM, ESS, Eclipse+StatET, RStudio or RevolutionR among others.
You can run grep 'a<-' .Rhistory from terminal (assuming that you've cdd to your working directory). ESS has several very useful history-searching functions, like (comint-history-isearch-backward-regexp) - binded to M-r by default.
For further info, consult ESS manual: http://ess.r-project.org/Manual/ess.html
When you define a function, R stores the source code of the function (preserving formatting and comments) in an attribute named "source". When you type the name of the function, you will get this content printed.
But it doesn't do this with variables. You can deparse a variable, which generates an expression that will produce the variable's value but this doesn't need to be the original expression. For example when you have b <- c(17, 5, 21), deparse(b) will produce the string "c(17, 5, 21)".
In your example, however, the result wouldn't be "c(vectorA,vectorB,vectorC)", it would be an expression that produces the combined result of your three vectors.