为什么我的 NMDS 绘图是拱形/马蹄形？

Question

我有一个数据集，其中包含每月采样的浮游动物数据。它始终针对同一采样点，因此不是空间上的，而是超过 10 年。我想使用 NMDS 图来查看 2014 年至 2024 年的浮游动物群落（三月、四月和五月期间）是否会使用 NMDS 分为不同的群落，但结果是拱形的。我可以解决这个问题吗？这些样本没有额外的环境变量。我使用了每个样本的总丰度（m-3）。

nmds <- metaMDS(dist_matrix, k = 2, trymax = 100)

stress_value<-nmds$stress

nmds_scores <- as.data.frame(scores(nmds))
nmds_scores$month <- Total_Abundance_Spring_Mero$Month
nmds_scores$year <- Total_Abundance_Spring_Mero$Year

# Plot NMDS
ggplot(nmds_scores, aes(x = NMDS1, y = NMDS2, color = factor(year), shape = factor(month))) +
  geom_point(size = 3) +
  labs(title = "Total abundance (m-3) of Meroplankton in Spring", x = "NMDS1", y = "NMDS2", color = "Year", shape = "Month") +
  theme_classic()+
  annotate("text", x = Inf, y = Inf, label = paste("Stress =", round(stress_value, 4)), 
           hjust = 1.1, vjust = 1.1, size = 5, color = "red")````

[Arch Shaped NMDS plot, shapes represent the month and color the year](https://i.sstatic.net/4aBN7ffL.png)

Answer 1

这是您未发布的代码部分的问题，或者是您的数据的问题。或者如何计算 dist_matrix。

如果我运行以下命令，我也会得到一个弧线。

library(vegan)
library(ggplot2)

Total_Abundance_Spring_Mero <- data.frame(
  Month = sample(1:12, 100, replace = TRUE), 
  Year = sample(2010:2020, 100, replace = TRUE), 
  n1 = 1:100,
  n2 = 1:100)

dist_matrix <- vegdist(Total_Abundance_Spring_Mero[, -c(1, 2)], method = "bray")

nmds <- metaMDS(dist_matrix, k = 2, trymax = 100)

stress_value<-nmds$stress

nmds_scores <- as.data.frame(scores(nmds))
nmds_scores$month <- Total_Abundance_Spring_Mero$Month
nmds_scores$year <- Total_Abundance_Spring_Mero$Year

# Plot NMDS
ggplot(nmds_scores, aes(x = NMDS1, y = NMDS2, color = factor(year), shape = factor(month))) +
  geom_point(size = 3) +
  labs(title = "Total abundance (m-3) of Meroplankton in Spring", x = "NMDS1", y = "NMDS2", color = "Year", shape = "Month") +
  theme_classic()+
  annotate("text", x = Inf, y = Inf, label = paste("Stress =", round(stress_value, 4)), 
           hjust = 1.1, vjust = 1.1, size = 5, color = "red")