carico dataframe

library(readxl)
SENSE <- read_excel("SENSE_rilievi floristici_AAB_Dataset.xlsx")

SISTEMAZIONE DATASET

#creo colonna replica temporale

library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
SENSE <- SENSE %>%
  mutate(temp_replica = case_when(
    DATE == "20230329" ~ 1,
    DATE == "20230427" ~ 2,
    DATE == "20230507" ~ 3,
    TRUE ~ NA_integer_
  )) %>%
  select(temp_replica, everything())

#Rinomino SENSE$`Plot `
SENSE <- SENSE %>%
  rename(Plot = `Plot `)

# CREO L'ID
SENSE <- mutate(SENSE,
             ID = paste(temp_replica,TREATMENT,Plot, sep = "_"))

#levo gli spazi dopo "TREATMENT"
library(stringr)
SENSE$ID <- str_replace_all(SENSE$ID," ", "")


# sposto la colonna
SENSE <- SENSE %>%
  select(ID, everything())

#elimino altre colonne e imposto rownames
sense <- as.data.frame(SENSE)
rownames(sense) <- sense$ID
sense$ID <- NULL

#divido il dataframe in due dataframe specie e env

sense_species <- sense %>% select(-(temp_replica:TOT))
sense_env <- sense %>% select(temp_replica:TOT)

# Supponiamo che il tuo dataframe si chiami sense_species
sense_species[is.na(sense_species)] <- 0

sense_env$temp_replica <- as.factor(sense_env$temp_replica)

#shannon e simpson

library(vegan)
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.6-4
# Calcola l'indice di diversità di Shannon per ogni rilievo
shannon_indices <- diversity(sense_species, index = "shannon")

# Calcola l'indice di diversità di Simpson per ogni rilievo
simpson_indices <- diversity(sense_species, index = "simpson")

tot_species <- sense_species[, 1:ncol(sense_species)]
species_richness <- specnumber(tot_species)

# Aggiungi i risultati al tuo dataframe originale
sense_env$shannon <- shannon_indices
sense_env$simpson <- simpson_indices
sense_env$richness <- species_richness

#BOXPLOT

library(ggplot2)
# Crea paired boxplots per Shannon
ggplot(sense_env, aes(x = TREATMENT, y = shannon, fill = temp_replica)) +
  geom_boxplot(position = "dodge") +
  labs(title = "Paired Boxplots: Shannon VS treatment Fill: temp_replica")

# Crea paired boxplots per Simpson
ggplot(sense_env, aes(x = TREATMENT, y = simpson, fill = temp_replica)) +
  geom_boxplot(position = "dodge") +
  labs(title = "Paired Boxplots: Simpson VS treatment. Fill: temp_replica")

# Crea paired boxplots per Richness
ggplot(sense_env, aes(x = TREATMENT, y = richness, fill = temp_replica)) +
  geom_boxplot(position = "dodge") +
  labs(title = "Paired Boxplots: species richness VS treatment. Fill: temp_replica")