R语言绘制叶片腐烂养分时序图遇summarySE报错，绘图无数据点

问题 #

我正在制作一个R程序，用于绘制叶片腐烂过程中养分随时间变化的数据图。使用R 4.3.2，在Visual Studio和R可执行文件中均遇到相同问题。

代码 #

library(ggplot2)
library(dplyr)
library(patchwork)
library(Rmisc)

Nutrient_data <- read.csv("C:\\Users\\MyName\\Downloads\\Nutrient_data.csv")

Nitrite_plotdat <- Nutrient_data %>% filter(Site=="Nitrite")
Orthophosphate_plotdat <- Nutrient_data %>% filter(Site=="Orthophosphate")

Nitrite_plotdat <- summarySE(data = Nitrite_plotdat, measurevar = "Quality", groupvars = "Site", na.rm = TRUE)
Orthophosphate_plotdat <- summarySE(data = Orthophosphate_plotdat, measurevar = "Quality", groupvars = "Site", na.rm = TRUE)

p_Nitrite <- ggplot(Nitrite_plotdat, aes(x = Site, y = Nitrite)) + 
  geom_bar(stat = "identity") + 
  geom_errorbar(aes(ymin = Nitrite - se, ymax = Nitrite + se), width = 0.2) + 
  theme_classic()

p_Orthophosphate <- ggplot(Orthophosphate_plotdat, aes(x = Site, y = Orthophosphate)) + 
  geom_bar(stat = "identity") + 
  geom_errorbar(aes(ymin = Orthophosphate - se, ymax = Orthophosphate + se), width = 0.2) + 
  theme_classic()

combined_plot <- p_Nitrite + p_Orthophosphate
combined_plot


# n_model <- aov(nitrate_sum$Quality~nitrite_sum$Site)
# summary(n_model)
# o_model<- aov(orthophosphate_sum$Quality~orthophosphate_sum$Site)
# summary(o_model)

错误信息 #

运行代码时，第11、12行出现如下错误：

> Nitrite_plotdat <- summarySE(data = Nitrite_plotdat, measurevar = "Quality",$
The following `from` values were not present in `x`: mean
> Orthophosphate_plotdat <- summarySE(data = Orthophosphate_plotdat, measureva$
The following `from` values were not present in `x`: mean

生成的图表有正确的坐标轴，但没有绘图点。

CSV数据片段 #

Day,Group,Site,Nitrite,Orthophosphate,,SE Nitrite,SE Orthophosphate,,,SD Nitrite,SD Orthophosphate

Monday,1,Townhouse_pond,0.002,0.37,,0.000812409,0.153933338,,,0.005914424,1.088473073

Monday,1,St_Johns_upstream,0.001,0.21,,,,,,,

Monday,1,St_Johns_downstream,0.007,0.11,,,,,,,

Monday,2,Townhouse_pond,0.002,0.53,,,,,,,

Monday,2,St_Johns_upstream,0.003,0.23,,,,,,,

Monday,2,St_Johns_downstream,0.003,0.17,,,,,,,

Monday,3,Townhouse_pond,0.005,0.56,,,,,,,

Monday,3,St_Johns_upstream,0.009,0.2,,,,,,,

Monday,3,St_Johns_downstream,0.016,0.24,,,,,,,

Monday,4,Townhouse_pond,0.013,0.57,,,,,,,

Monday,4,St_Johns_upstream,0.007,0.19,,,,,,,

Monday,4,St_Johns_downstream,0.01,0.17,,,,,,,

Tuesday am,1,Townhouse_pond,0.001,0.57,,,,,,,

Tuesday am,1,St_Johns_upstream,0.009,6.3,,,,,,,

已确认库导入正确，尝试了所有能想到的修复方法，恳请提供进一步的建议和帮助。

解决方案 #

核心问题分析 #

1. 数据过滤逻辑错误：CSV中Site列是采样点名称（如Townhouse_pond），而非养分类型（Nitrite/Orthophosphate），用filter(Site=="Nitrite")会过滤掉所有数据，导致summarySE处理空数据集引发错误。
2. summarySE参数错误：measurevar指定了不存在的Quality列，实际应统计Nitrite或Orthophosphate；groupvars仅设为Site无法体现时间维度的变化，需按Day+Site分组。
3. 绘图映射错误：空数据集无法生成绘图元素，且后续绘图的y轴映射逻辑不符合summarySE的输出结构。

修复步骤 #

步骤1：修正数据处理逻辑

library(ggplot2)
library(dplyr)
library(patchwork)
library(Rmisc)

# 读取数据并移除空列（CSV中存在多个无意义空列）
Nutrient_data <- read.csv("C:\\Users\\MyName\\Downloads\\Nutrient_data.csv", na.strings = "") %>%
  select(-c(X, X.1, X.2))  # 移除自动命名的空列

# 按时间+采样点分组，统计亚硝酸盐的均值和标准误
Nitrite_plotdat <- summarySE(data = Nutrient_data,
                             measurevar = "Nitrite",
                             groupvars = c("Day", "Site"),
                             na.rm = TRUE)

# 按时间+采样点分组，统计正磷酸盐的均值和标准误
Orthophosphate_plotdat <- summarySE(data = Nutrient_data,
                                    measurevar = "Orthophosphate",
                                    groupvars = c("Day", "Site"),
                                    na.rm = TRUE)

步骤2：修正绘图代码

# 亚硝酸盐时间变化图
p_Nitrite <- ggplot(Nitrite_plotdat, aes(x = Day, y = Nitrite, fill = Site)) +
  geom_bar(stat = "identity", position = position_dodge(width = 0.8)) +
  geom_errorbar(aes(ymin = Nitrite - se, ymax = Nitrite + se),
                width = 0.2, position = position_dodge(width = 0.8)) +
  labs(title = "亚硝酸盐浓度随时间变化", y = "浓度") +
  theme_classic() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

# 正磷酸盐时间变化图
p_Orthophosphate <- ggplot(Orthophosphate_plotdat, aes(x = Day, y = Orthophosphate, fill = Site)) +
  geom_bar(stat = "identity", position = position_dodge(width = 0.8)) +
  geom_errorbar(aes(ymin = Orthophosphate - se, ymax = Orthophosphate + se),
                width = 0.2, position = position_dodge(width = 0.8)) +
  labs(title = "正磷酸盐浓度随时间变化", y = "浓度") +
  theme_classic() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

# 合并图表并统一图例
combined_plot <- p_Nitrite + p_Orthophosphate + plot_layout(guides = "collect")
combined_plot

步骤3：方差分析代码修正（可选）

# 亚硝酸盐方差分析（时间和采样点作为因子）
n_model <- aov(Nitrite ~ Day + Site, data = Nutrient_data)
summary(n_model)

# 正磷酸盐方差分析
o_model <- aov(Orthophosphate ~ Day + Site, data = Nutrient_data)
summary(o_model)

额外说明 #

• 若不想用summarySE重新计算，可直接使用CSV中已有的SE Nitrite、SD Nitrite列，但需确保数据与分组逻辑对齐。
• 若更侧重时间趋势展示，可将geom_bar替换为geom_line+geom_point，更直观体现变化。

内容的提问来源于stack exchange，提问作者Blake