Regarding stock trains or stock extras as they were sometimes referred to:
I know that SR's Harrisonburg Branch had them and that 27 or so miles away in Potomac Yard there were stock pens at one time, not to mention stock pens at many of the stations along the line. They also had icing platforms for the reefers and I suspect those may have also been used to cool off the subjects of this discussion sometimes in summer.
There were certain rules to be followed regarding these special trains, chiefly as I recall that the cars had to halted at least every 24 hours and emptied and the animals given a chance not just to be fed and watered but also cooled for at least 24 hours before proceeding to the next location in their travels.
Many of the stations had quite extensive stock pens as the local farmers would drive their herds literally to market or the local pen in this case. Harrisonburg as one place in particular even still has auctions but of course those animals are brought and taken away by truck.
By the early 1950's the practice of the stock trains and extras had become far fewer and by the late 1950's I have been told, were the last such trains for whatever the animals were: cattle, hogs, sheep, maybe even horses.
If you know where to look along that 111 mile long line even today, you can figure out where some of these once important things were located. Many have long since disappeared. In Mt. Jackson in the 1917 period I seem to recall, health issues started to become a factor as the odor (putting it mildly here) as well as the leftovers from the animals had become a serious problem. Other depots like New Market were several miles out of town and that presented less of a problem. However when the wind blew JUST right ........ oh never mind, you can get the idea.
Further south in the area south of Broadway, the Daphna valley region, used to be sheep country and I am told, still is. In Linville, the next depot south from there and the last before Harrisonburg is even today, rendering plant where the station once was.