In World War I, there was a need for transportation. What agency/leader was in charge of making changes?

I assume that the agency that you are talking about is the
United States Railroad Administration.  This was an agency set up during World War I to
try to ensure that the railroads (the major method of transportation at that time) would
run smoothly.

At the beginning of WWI, both the railroad
companies and the railroad unions were doing things that made it hard for the railroads
to operate efficiently.  The companies wanted to continue to make lots of money and the
unions wanted to force higher wages.  Even when railroads cooperated, there was the
problem of antitrust legislation that made it so that such actions were possibly
illegal.

To get around all of these problems, Pres. Wilson
simply nationalized the railroads.  From that point on, the government ran the
railroads.  It did so in order to make sure that men and materiel would be able to make
it to ports in order to be shipped off to Europe.