计算每周每个物种的平均发芽率

Question

我得到了一个数据集，每周记录不同物种（Species）的种子在不同土壤类型（Soil_origin）中的发芽情况。我为每个物种准备了四个复制品，换句话说：对于每个物种 x 土壤类型，我有四个容器，每个容器包含十个种子。我想计算每个物种 x 土壤类型每周的平均发芽率（因此平均值 n=4）。

我不知道如何将我的数据集包含在这个脚本中...

我希望你能帮我解决这个问题！

感谢您的宝贵时间。

### My dataset is too large, therefore here I only included the first 10 rows...


> dput(head(Data_bakken_R, 10))
structure(list(Soil_origin = c("P_c", "P_c", "P_c", "P_c", "P_c", 
"P_c", "P_c", "P_c", "P_c", "P_c"), Species = c("C_flava", "C_flava", 
"C_flava", "C_flava", "C_flacca", "C_flacca", "C_flacca", "C_flacca", 
"C_panicea", "C_panicea"), Pot = c(1, 2, 3, 4, 1, 2, 3, 4, 1, 
2), Date = structure(c(1685664000, 1685664000, 1685664000, 1685664000, 
1685664000, 1685664000, 1685664000, 1685664000, 1685664000, 1685664000
), tzone = "UTC", class = c("POSIXct", "POSIXt")), Day_since_cooling = c(6, 
6, 6, 6, 6, 6, 6, 6, 6, 6), Total_start = c(10, 10, 10, 10, 10, 
10, 10, 10, 10, 10), Germinated = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
0)), row.names = c(NA, -10L), class = c("tbl_df", "tbl", "data.frame"
))

### Install packages 
install.packages("ggplot2")
library(ggplot2)

install.packages("zoo")
library(zoo)

install.packages('tidyverse')
library(tidyverse)

### Plot per soil type
Data_bakken_R %>% 
  mutate(Proportion_germination = Germinated/Total_start) %>%
  ggplot(aes(x = Day_since_cooling, y = Proportion_germination, color = Soil_origin)) +
  geom_line() +
  facet_grid(rows = vars(Species)) +
  labs(x = "Time (days)", y = "Proportion of germinated seeds") + theme_classic() + ylim (0.0, 1.0)  `

Answer 1

可能将

grup_by()

与

week()

一起使用：

Data_bakken_R %>% 
  mutate(weeknum = week(Date)) %>% 
  group_by(Soil_origin, Species, Day_since_cooling, weeknum) %>% 
  summarise(Proportion_germination = sum(Germinated)/sum(Total_start)) %>% 
  ggplot(aes(x = Day_since_cooling, y = Proportion_germination, color = Soil_origin)) +
  geom_line() +
  facet_grid(rows = vars(Species)) +
  labs(x = "Time (days)", y = "Proportion of germinated seeds") + theme_classic() + ylim (0.0, 1.0)  

但是我不知道如何处理

Day_since_cooling

，因为你在问题中没有提到它。这就是为什么我也将这个变量添加到分组中。