You could also try Statistics::R to control your R interpreter from Perl, i.e. you'd create the command strings on the Perl side and use $R->send($cmd) to execute them.  Something like this:

use Statistics::R;
 
my $R = Statistics::R->new();
$R->startR;

for my $i (1..100) {
    $R->send( << "EOR";
g <- read.graph("filename$i.net", "pajek")
d <- degree (g, mode="in")
power.law.fit (d+1, 2)
EOR
)}
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