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A pen is an area created specifically to contain farm animals. Pens can be created with a mixture of fences and fence gates, barricades, solid walls (constructed or naturally occurring) and/or doors. Animal flaps can be used to provide indoor sections to a pen that animals can move freely into and out of without leaving or compromising the pen. Pens can be designated for different types of animals (see below), and colonists assigned to the Animals work will automatically rope wandering tamed farm animals and lead them to a pen. Roped animals can only pass through fence gates. Animals in a pen will be passive and will not attack hostiles, and vice versa.
Pens are good, but not perfect, protection against predatory wild animals, which will happily kill your tamed animals for a quick meal. Predators that are outside a pen will not target penned animals on the other side of a pen's fence/barrier, but if it randomly wanders over a barrier and into the pen, then it can. An alert will be given when a predator has wandered into a pen that is currently in use. Be aware that all animals except pennable animals will wander the map randomly, and will occasionally enter a pen by jumping over a fence or gate.
Unpenned farm animals cannot be assigned to an area like humans and pets, and will roam around, producing large amounts of filth, which is reduced by a factor of x0.05 by the straw matting floor. A minor, permanent warning will appear, reminding you to either pen the animal or place straw matting. They will also occasionally attempt to roam off the map, determined by the roam interval stat. The game will also give a temporary warning in the top left of the screen if this happens.
All the animals that can be kept in a pen are listed in the "Animals" tab of the Pen Marker UI. Only herbivores are allowed into the Pen, so: Cows, Horses, Boomalopes, Yaks,... to name a few.
A pen marker is an important part of a pen, and is quickly built for only 30 stuff. It designates what animals are to be put inside the pen; until you place a pen marker, no animals will be hauled there. Pen markers also give you additional information and control over each separate pen area (see below). It does not matter where in the pen you place the pen marker; put it somewhere you can easily find it again to refer to it when you need to.
Clicking on a pen marker will show three buttons, each containing useful information and configurations for a pen. The first tab is used to configure which species of animal is allowed in the pen. The second shows how many animals a pen can sustain without colonist intervention (through grass and brambles that grow naturally), measured in cows, goats, and chickens, including an option to force display other animals in the count. The third tab allows you to set up auto-cut orders for plants. You can also set up an auto-slaughter order in the animals tab that sets a slaughter job for animals when the count of a certain gender and species surpasses a set number. Juvenile animals are not included in this count, but pregnant animals can be allowed. The auto-slaughter will mark animals in the order of oldest to youngest, and will mark pregnant animals (if allowed) in the order of their pregnancy (most recent to least recent).
For a place to be considered a pen it should be a closed area surrounded by barriers:(walls, doors, fences or fence gates), with at least one animal-suitable entrance (i.e. fence gate) to lead animals in. A pen marker is also required and serves as a stat display when selected. Unless these conditions are met, an area is not recognized as a "pen" and colonists won't begin to rope tamed pen animals in.
Marking the pen area as a separate "zone" manually is not required, it's handled by the pen marker as long as the conditions above are met.
A room separated from the pen with an animal flap instead of a door will count as part of the attached pen, and extreme temperatures can be harmful for animals. Depending on the season and biome, building a barn (a walled area with roof and animal flap for a door) with controlled temperature inside a pen can be a good precaution against severe temperatures. Place animal sleeping spots inside the barn (place lots, for future births/additions). If you want to place a floor in a barn, best use straw matting to minimize filth generated by farm animals (with appropriate fire precautions).
Sustenance and size planning
Different animals require a different amount of food, and this information can be read on the pen marker "Food" tab. An adult pig (0.8) or a cow (0.86) consumes much more than, say, a sheep (0.36) and thus requires a bigger pen to survive. Pens tend to be large more often than not (a 20x20 pen on a normal soil in Temperate forest holding grass can barely maintain 4 adult pigs), and since animals tend to multiply, it's good to have reserve space.
Amount of sustenance (grass, brambles, plants etc) inside a pen does not depend on the size alone but rather on the amount of vegetation present inside. Consequently, a pen set on stony soil without grass will give little to no sustenance. Moreover, amount of food available is dynamic, which can be seen by viewing Pen marker: sometimes an animal consumes a tile of grass, reducing overall quantity. In warm biomes supporting growing, grass and other vegetation also gradually regrow, albeit slowly (and not in cold seasons), which may or may not compensate consumption. Consider "switching" animals between different pens if you have enough space to allow time to regrow. Additionally, while you can't grow grass directly (outside of Dev console), you can plant flowers (such as dandelions) which count as valid grazing.
Animals graze on grass and other vegetation, but normally not on trees, so trees contribute nothing to sustenance and can be safely cut. Avoid planting common human crops and hay intended for storage inside a pen since many animals consider live plants as valid food and can damage your farm. Wildfires can destroy vegetation quickly: keep them in check to avoid damage to your pen!
Outdoor plants usually freeze when it's too cold outside and animals can't use normal vegetation in a pen for food any more. Consider stocking on Hay and/or Kibble if you want your livestock to survive through the winter and mind their dietary needs to avoid starvation.
When receiving items from an orbital trader, the drop pods will not go into pens. Presumably this was implemented to prevent pen animals from eating your goods. This can result in undesirable drop locations if you have a very large pen and/or a mountainous base - it's even possible to not receive your items. If this happens, simply make an unpenned area so that the drop pods can land.