Однодольные

Загрузка данных

knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
library(tidyverse)
library(readxl)
library(vegan)
df <- read_xlsx("Однодольные_для_перманова.xlsx") %>% 
  select(-Семейство, -Вид)

1. Полный набор данных

A. Все семейства

dist1a <- vegdist(df[,2:13], method = "euclidean")
adonis(dist1a ~ Fam, data = df, permutations = 9999)

## 
## Call:
## adonis(formula = dist1a ~ Fam, data = df, permutations = 9999) 
## 
## Permutation: free
## Number of permutations: 9999
## 
## Terms added sequentially (first to last)
## 
##           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## Fam        3    489.98 163.326  104.87 0.84661  1e-04 ***
## Residuals 57     88.77   1.557         0.15339           
## Total     60    578.75                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

B. Два семейства

dist1b <- filter(df, Fam %in% c("Iri", "Poa"))[,2:13]
dist1b <- vegdist(dist1b, method = "euclidean")
adonis(dist1b ~ Fam, 
       data = filter(df, Fam %in% c("Iri", "Poa")), 
       permutations = 9999)

## 
## Call:
## adonis(formula = dist1b ~ Fam, data = filter(df, Fam %in% c("Iri",      "Poa")), permutations = 9999) 
## 
## Permutation: free
## Number of permutations: 9999
## 
## Terms added sequentially (first to last)
## 
##           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## Fam        1    22.338 22.3381  16.761 0.44388  1e-04 ***
## Residuals 21    27.987  1.3327         0.55612           
## Total     22    50.325                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

2. Два ключевых признака

A. Все семейства

dist2a <- df %>% select(D, L_RH) %>% 
  vegdist(method = "euclidean")
adonis(dist2a ~ Fam, data = df, permutations = 9999)

## 
## Call:
## adonis(formula = dist2a ~ Fam, data = df, permutations = 9999) 
## 
## Permutation: free
## Number of permutations: 9999
## 
## Terms added sequentially (first to last)
## 
##           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## Fam        3   107.251  35.750  207.53 0.91613  1e-04 ***
## Residuals 57     9.819   0.172         0.08387           
## Total     60   117.070                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

ggplot(df, aes(x = D, y = L_RH, color = Fam)) + 
  geom_point() + 
  scale_color_manual(values = c("green", "steelblue2", "plum1", "yellow1")) +
  stat_ellipse()+
  theme_classic() + 
  theme(legend.position = "bottom")

B. Два семейства

dist2b <- df %>% 
  filter(Fam %in% c("Iri", "Poa")) %>% 
  select(D, L_RH) %>% 
  vegdist(method = "euclidean")
adonis(dist2b ~ Fam, 
       data = filter(df, Fam %in% c("Iri", "Poa")), 
       permutations = 9999)

## 
## Call:
## adonis(formula = dist2b ~ Fam, data = filter(df, Fam %in% c("Iri",      "Poa")), permutations = 9999) 
## 
## Permutation: free
## Number of permutations: 9999
## 
## Terms added sequentially (first to last)
## 
##           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## Fam        1    4.1122  4.1122  15.388 0.42289  3e-04 ***
## Residuals 21    5.6119  0.2672         0.57711           
## Total     22    9.7241                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

ggplot(filter(df, Fam %in% c("Iri", "Poa")), aes(x = D, y = L_RH, color = Fam)) + 
  geom_point() + 
  scale_color_manual(values = c("steelblue2", "yellow1")) +
  stat_ellipse()+
  theme_classic() + 
  theme(legend.position = "bottom")

3. Два виртуальных признака

A. Все семейства

dist3a <- df %>% select(F_размер, F_другое) %>% 
  vegdist(method = "euclidean")
adonis(dist3a ~ Fam, data = df, permutations = 9999)

## 
## Call:
## adonis(formula = dist3a ~ Fam, data = df, permutations = 9999) 
## 
## Permutation: free
## Number of permutations: 9999
## 
## Terms added sequentially (first to last)
## 
##           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
## Fam        3   101.451  33.817  103.92 0.84542  1e-04 ***
## Residuals 57    18.549   0.325         0.15458           
## Total     60   120.000                 1.00000           
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

ggplot(df, aes(x = F_размер,    F_другое, color = Fam)) + 
  geom_point() + 
  scale_color_manual(values = c("green", "steelblue2", "plum1", "yellow1")) +
  stat_ellipse()+
  theme_classic() + 
  theme(legend.position = "bottom")

B. Два семейства

dist3b <- df %>% 
  filter(Fam %in% c("Iri", "Poa")) %>% 
  select(F_размер,  F_другое) %>% 
  vegdist(method = "euclidean")
adonis(dist3b ~ Fam, 
       data = filter(df, Fam %in% c("Iri","Poa")), 
       permutations = 9999)

## 
## Call:
## adonis(formula = dist3b ~ Fam, data = filter(df, Fam %in% c("Iri",      "Poa")), permutations = 9999) 
## 
## Permutation: free
## Number of permutations: 9999
## 
## Terms added sequentially (first to last)
## 
##           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)  
## Fam        1    2.1558 2.15577  5.8602 0.21817 0.0106 *
## Residuals 21    7.7252 0.36787         0.78183         
## Total     22    9.8810                 1.00000         
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

ggplot(filter(df, Fam %in% c("Iri","Poa")), aes(x = F_размер, y = F_другое, color = Fam)) + 
  geom_point() + 
  scale_color_manual(values = c("steelblue2", "yellow1")) +
  stat_ellipse()+
  theme_classic() + 
  theme(legend.position = "bottom")