Filogenia

# Cargar las bibliotecas necesarias
library(phyloseq)

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library(ggplot2)

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library(vegan)

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library(DESeq2)

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R Markdown

# Asegurarse de que la columna de grupo está presente en sample_data(datos)
sample_data(datos)$Group <- sample_data(datos)$Estado_de_salud

# 1. Análisis de la diversidad alfa y generación de tests estadísticos
# Calcular métricas de diversidad alfa
diversity_alpha <- estimate_richness(datos, measures = c("Observed", "Shannon", "Simpson"))
diversity_alpha$Group <- sample_data(datos)$Group

# Gráfico de la diversidad alfa (Shannon Index)
ggplot(diversity_alpha, aes(x = Group, y = Shannon)) +
  geom_boxplot() +
  geom_jitter(width = 0.2) +
  theme_minimal() +
  labs(title = "Alpha Diversity (Shannon Index)", x = "Group", y = "Shannon Index")

# Prueba estadística de la diversidad alfa (Shannon Index)
wilcox.test(Shannon ~ Group, data = diversity_alpha)

## 
##  Wilcoxon rank sum exact test
## 
## data:  Shannon by Group
## W = 13, p-value = 0.007621
## alternative hypothesis: true location shift is not equal to 0

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