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== Passing arguments to R scripts == | == Passing arguments to R scripts == <!--T:84--> | ||
Sometimes it can be useful to pass parameters as arguments to R scripts, to avoid having to either change the R script for every job or having to manage multiple copies of otherwise identical scripts. This can be useful to specify the names for input- or output-files, or maybe numerical parameters. | Sometimes it can be useful to pass parameters as arguments to R scripts, to avoid having to either change the R script for every job or having to manage multiple copies of otherwise identical scripts. This can be useful to specify the names for input- or output-files, or maybe numerical parameters. | ||
<!--T:85--> | |||
The following example expects exactly two arguments. The first one should be a string which will be used for the variable "name" and the second one should be an integer for the variable "number". | The following example expects exactly two arguments. The first one should be a string which will be used for the variable "name" and the second one should be an integer for the variable "number". | ||
{{File | {{File | ||
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args = commandArgs(trailingOnly=TRUE) | args = commandArgs(trailingOnly=TRUE) | ||
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# test if there is at least two arguments: if not, return an error | # test if there is at least two arguments: if not, return an error | ||
if (length(args)<2) { | if (length(args)<2) { | ||
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} | } | ||
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name <- args[1] # read first argument as string | name <- args[1] # read first argument as string | ||
number <- as.integer( args[2] ) # read second argument as integer | number <- as.integer( args[2] ) # read second argument as integer | ||
<!--T:88--> | |||
print(paste("Processing with name:'", name, "' and number:'", number,"'", sep = '')) | print(paste("Processing with name:'", name, "' and number:'", number,"'", sep = '')) | ||
}} | }} | ||
<!--T:89--> | |||
This script can be used like this: | This script can be used like this: | ||
{{Command | {{Command | ||