nipype.interfaces.r module¶
Interfaces to run R scripts.
RCommand¶
Bases: CommandLine
Interface that runs R code
>>> import nipype.interfaces.r as r >>> r = r.RCommand(rfile=False) >>> r.inputs.script = "Sys.getenv('USER')" >>> out = r.run()
- Mandatory Inputs
script (a string) – R code to run. Maps to a command-line argument:
-e "%s"
(position: -1).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)rfile (a boolean) – Run R using R script. (Nipype default value:
True
)script_file (a pathlike object or string representing a file) – Name of file to write R code to. (Nipype default value:
pyscript.R
)
- RCommand.set_default_r_cmd(r_cmd)¶
Set the default R command line for R classes.
This method is used to set values for all R subclasses.
- RCommand.set_default_rfile(rfile)¶
Set the default R script file format for R classes.
This method is used to set values for all R subclasses.
- nipype.interfaces.r.get_r_command()¶