The school has also decided to cancel classes on Friday, November 16.
The decision came after University officials noticed the air quality was getting worse through the day. University officials said they consulted both Campus and Merced County Public Health officials and decided to err on the side of caution.
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"We're on a campus like this where people have to walk outside on a regular basis," said Vice Chancellor of Student Affairs Charles Nies.
"Our concern was that we couldn't give that medical recommendation to stay indoors if students were going to be forced to walk outside."
A long line of cars stretched out in front of the campus as people started to leave. Students could be seen wearing masksas they headed back to their cars.
"I can smell it and I have migraines so the bad air quality does trigger migraines for me," said Krystalynn Williams, a UC Merced student.
Dr. David Canton with the Merced County public health department said while the air quality isn't as bad as it could be, he still recommended that residents stay indoors.
"For the average person, it's an irritant, its not necessarily harmful per se," Canton said.
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"But if you get enough particulate into your lungs, it causes inflammation, reactions, potential infections. Somebody prone to developing asthma could develop asthma."
University officials said that while most services are closed, some essential services, like the dining hall and residence halls, remained open.
The university is treating this like an emergency, so hourly workers are still going to be paid for a full day's work. University health officials were also giving students masks to wear prior to canceling classes.