tapply(set1$coral.cover,list(set1$site,set1$survey_year),mean)

Error in tapply(set1$coral.cover, list(set1$site, set1$survey_year), mean) :
  arguments must have same length

set1 <- data.frame(coral.cover = sample(1:100, 100, replace=TRUE),
                   coral.column = sample(1:3, 100, replace=TRUE),
                   site = paste0("site ",sample(1:5, 100, replace=TRUE)),
                   survey_year = sample(2010:2017, 100, replace=TRUE))

str(set1)
tapply(set1$coral.cover,list(set1$site,set1$survey_year),mean)

> str(set1)
'data.frame':   100 obs. of  4 variables:
 $ coral.cover : int  63 35 42 15 60 65 63 59 7 55 ...
 $ coral.column: int  2 2 3 1 1 3 2 2 3 3 ...
 $ site        : Factor w/ 5 levels "site 1","site 2",..: 5 1 5 3 1 2 2 1 4 4 ...
 $ survey_year : int  2011 2016 2014 2016 2017 2014 2012 2010 2013 2015 ...

> tapply(set1$coral.cover,list(set1$site,set1$survey_year),mean)
        2010 2011     2012     2013 2014 2015     2016 2017
site 1 52.50   14 64.50000 71.00000 60.0 64.5 42.33333 60.0
site 2 48.00   11 45.75000  4.00000 64.0 74.0 63.00000   NA
site 3 29.00   15       NA 66.20000 39.8 68.0 34.00000 61.6
site 4    NA   NA 49.00000 63.33333 24.0 47.0 35.00000 81.0
site 5 42.25   58 43.16667 38.00000 37.0 40.0 54.50000   NA