The pigs used to validate the protocol were part of studies approved by The Animal Experimental Council – a national governmental institution evaluating and approving all animal experiments in Denmark. The Council does the ethical review similar to an IACUC.

1. Arrival at the research facility

1. First, wash the pigs in a designated area to allow a thorough visual inspection. Use an exclusion list to exclude pigs with wounds, ear bites, abscesses, lameness etc., so only animals that appear clinically healthy are allowed into the facility.
2. After washing, sort the pigs into groups according to color marks. The color marks indicate which pigs have been pen mates at the supplier. This is important since pigs will fight to establish a hierarchy when they are introduced to new pen mates. Keeping them sorted in groups together with pigs they are already familiar with limits this fighting considerably.
3. Leave the pigs undisturbed (except when they are fed in the afternoon) for the rest of the arrival day as they can be quite stressed after transportation.

2. Part one: The transition phase (estimated time 4-6 days)

NOTE: The pigs stay in their home pen during the activities performed in the transition phase. We use half an apple for each treat-session. The progress of each individual pig is scored in the Transition Phase Progression Checklist (Figure 1 and Supplementary File 1).

1. On the two consecutive days after arrival, introduce the treats.
   1. Toss treats a few at a time (half apple total) into the pen twice daily to allow the pigs to search for the treats on their own and stand quietly just outside the pen. Apart from becoming familiar with treats, the goal is for the animal to positively associate the treat with the presence of a caretaker.
2. On day three and successive days introduce familiarizing the pig with "handling by a caretaker". Enter the pen during feeding.
   1. Sit down at arm's length from the pig while it is eating (Figure 3). Calmly extend a hand towards the pig to touch its back. The touch should be more than two seconds to count as successful. If the pig backs away from the food, withdraw the hand slowly.
   2. Wait until the animal commences eating and perform the action again. If the animal backs away from the food again, stop trying to touch it but remain inside the pen next to the trough (2-3 minutes in total for the session).
3. Move on in the handling procedure when the pig accepts being touched on the back while it is eating. Now move the hand around on the back in both direction of the head and the tail.
   1. Touch the head and ears if the pig accepts it. If at any time, the pig backs away from an action stop the action but remain inside the pen for the remaining time (2-3 minutes in total for the session). The ear is important as it enables blood sampling from an intravenous catheter in the ear.
   2. Rise slowly to be able to touch the tail region which is the second important area. Standing and moving about is more frightening to the pig, which is why this step is scored independently. When the pig accepts having the area touched and the tail manipulated, a rectal temperature can be taken to support most research protocols.
4. To further strengthen the bond between caretaker and animal enter the pen during two sessions apart from the feeding times. Offer the pig treats (one slice at a time) during two sessions (2-3 minutes each), while sitting in a corner inside the pen. At first, give the treats from an outstretched arm, but decrease the distance gradually so the pig needs to come closer to get its reward.
5. The final stage of the transition phase is being able to touch the pig in the specific areas of the body and using only a few treats to do so. Enter the pen while a second caretaker stands outside the pen and offers a treat or two to the pig. Reward the pig for being calm and allowing touching as described and at the same time being capable of keeping all four hoofs on the ground (not jumping up on the fence of the pen).

3. Part two: Commencing clicker training

NOTE: Following the transition phase, the animals are ready to start the clicker training. It is recommended that the training is performed in a designated area as it helps the pig to recognize that a training session is about to begin. Several short sessions across the day are better than one longer session.

1. Take one pig at a time outside the home pen and into the designated training area. If the area used is novel to the pig, the first sessions should be without training and strictly exploratory with a few treats during about 5-7 minutes exploration per pig.
2. Introduce the clicker sitting or standing with the treats out of reach of the pig. Click when the pig shows interest, and immediately give a treat. Do this in quick succession while the pig maintains interest. If the pig loses interest, pause the click-and-treat until the pig makes contact again. This session should be no longer than 10 minutes.
3. The pig will understand the click quickly, but it is important to make the association between click and treat very strong. Repeat the step a few sessions in a row to make the association between click and treat strong. Test if the pig associates the click with a treat by clicking once and not following this with a treat and monitoring the behavior of the pig closely. If the pig looks around eagerly expecting the treat, the training is complete, if not perform a few additional sessions.
4. Once the click is known by the pig, introduce the target stick. A target stick is a stick with a marked area on one end. Hold the target end in the height of the snout. At some point, the pig will touch it out of curiosity. Click in the very second that the pig touches the target and give a treat.
5. Present the target again immediately and if touched click again and give a treat. Continue the target training until the pig understands that it will be rewarded for touching the target. Move the target gradually further away so the pig has to move further to get to the target.
6. When the pig follows the target when it is moved around add additional challenges by putting objects into the training area, so the pig has to concentrate harder on the target stick task to get its rewards.