R: Replacing NA values by mean of hour with dplyr

Try

  shop.data %>% 
             group_by(hour) %>% 
             mutate(profit= ifelse(is.na(profit), mean(profit, na.rm=TRUE), profit))

  #   day hour profit
  #1   1    8    100
  #2   1   16    200
  #3   2    8     50
  #4   2   16     60
  #5   3    8     75
  #6   3   16    130

Or you could use replace

  shop.data %>% 
            group_by(hour) %>%
            mutate(profit= replace(profit, is.na(profit), mean(profit, na.rm=TRUE)))

A (less elegant) approach with base functions:

transform(shop.data, 
          profit = ifelse(is.na(profit), 
                          ave(profit, hour, FUN = function(x) mean(x, na.rm = TRUE)), 
                          profit))

#   day hour profit
# 1   1    8    100
# 2   1   16    200
# 3   2    8     50
# 4   2   16     60
# 5   3    8     75
# 6   3   16    130