这可能会给予预期的结果。
首先sumSpecies，然后构造 Comparison 字符串，最后进行除法运算，filter得到最终结果。

library(dplyr)

df %>% 
  summarize(Biomass_sum = sum(Biomass), .by = c(Paper, Condition)) %>% 
  mutate(Comparison = paste("Control vs", Condition),
         Biomass_results = Biomass_sum / 
           Biomass_sum[Comparison == "Control vs Control"], .by = Paper) %>% 
  filter(Comparison != "Control vs Control") %>% 
  select(-c(Biomass_sum, Condition))
  Paper          Comparison Biomass_results
1    P1 Control vs Species1       0.5000000
2    P2 Control vs Species4       5.0000000
3    P3 Control vs Species1       1.0000000
4    P3 Control vs Species2       4.0000000
5    P3 Control vs Species3       3.0000000
6    P3 Control vs Species4       3.5000000
7    P3 Control vs Species5       1.0000000
8    P4 Control vs Species6       0.3333333

数据

df <- structure(list(Paper = c("P1", "P1", "P1", "P2", "P2", "P2", 
"P3", "P3", "P3", "P3", "P3", "P3", "P4", "P4"), Biomass = c(10L, 
5L, 0L, 2L, 4L, 6L, 2L, 2L, 8L, 6L, 7L, 2L, 3L, 1L), Condition = c("Control", 
"Species1", "Species1", "Control", "Species4", "Species4", "Control", 
"Species1", "Species2", "Species3", "Species4", "Species5", "Control", 
"Species6")), class = "data.frame", row.names = c(NA, -14L))