PERTH AMBOY - With a graduation rate of only 58.97 percent, Perth Amboy High School's rate wasn't just the lowest in Middlesex County, it was one of the lowest in the state.

However, it wasn't a surprise, according to ousted superintendent Janine Caffrey.

"We saw all of this coming," Caffrey said. "By the time I arrived in Perth Amboy in 2011, about 200 students from the class of 2013 had already dropped out. As we learned more about student transfers, we realized we had been tracking incorrectly and would eventually see the results in our graduation rate."

Caffrey was about as polarizing a figure as you could find in Perth Amboy. Hired to be an agent of change in a struggling district, she found herself instead constantly battling with a Board of Education focused on removing her, something it did three times before she was finally relieved of her duties for good in October.

But regardless of what her critics may say, she had a front row seat for how the district ended up with one of the state's lowest graduation rates.

Perth Amboy had about 414 out of 702 students graduating. For perspective, the city of Camden's school district had a graduation of 53.42 percent, with 359 out of 672 students graduating.

Perth Amboy, like most other districts in the state, used to calculate graduation rates based on how many seniors graduated, Caffrey said.

The percentage was the number of students who got their diplomas, divided by the number of students who entered senior year. In Perth Amboy that meant a graduation rate well over 90 percent.

However, about three years ago the state began to move toward a new calculation method, one that is standard across the country.

This new way of calculating is based on each 9th grade cohort. The percentage is the number of students who earn diplomas divided by the total number of students who entered 9th grade four years prior to the June graduation.

The state also calculates a five year rate allowing for students who complete their credits a little later. This type of calculation depends upon careful tracking of student transfers so that each school is only accountable for students who actually continue attending their school.

Perth Amboy High School only used student self reporting until the 11-12 school year, when NJSMART data could be considered, according to Caffrey.

"During the summer of 2012 our Board of Education very wisely decided to investigate how it was calculating transfers," Caffrey said. "They hired former Commissioner of Education William Librera to conduct a complete review of the district's student information systems to ensure we were entering and tracking data accurately. It was determined that many students who were thought to be transfers were actually drop-outs.

"Additionally, it was determined that the school's computer system had been inaccurately rounding failing grades up to Ds. It was also discovered that many students who graduated failed to meet state attendance requirements."

What that means is 90 students who graduated in 2012 would not have if they had been held to attendance and grading standards, according to Caffrey.

"It was also standard practice prior to 2012 that students could make up academic credits by doing custodial work," Caffrey said. "I discovered this was occurring during summer school 2011, immediately after I was hired, and discontinued it. So the class of 2013 was the first class that had to come to school 90 percent of the time, get 60 percent or above to pass their courses, and was not permitted to make up credits through custodial work."

Caffrey said by the time she arrived in 2011 about 200 students from the class of 2013 had already dropped out.

"As we learned more about student transfers, we realized we had been tracking incorrectly and would eventually see the results in our graduation rate," Caffrey said. "Once we learned about the custodial work, computer rounding and attendance we anticipated very low numbers this year."