library(readr)
library(dplyr)
library(tidyverse)
library(nortest)
renvi <- read.csv("RiosEnvi.csv")
renvi$Land.use <- as.factor(renvi$Land.use)
renvi$Land.use1 <- as.factor(renvi$Land.use1)
renvi$River <- as.factor(renvi$River)
for (i in 5:ncol(renvi)) {renvi[[i]] <- as.numeric(renvi[[i]])}
str(renvi)
#PERMANOVA
library(vegan)
###Pairwise permanova
install.packages("remotes")
remotes::install_github("phytomosaic/ecole")
library(ecole)
#DO
adonis2(renvi$DO ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
set.seed(910)
permanova_pairwise(x = renvi$DO, grp =  renvi$Land.use, permutations = 999, padj = "bonferroni")
#Temperature
adonis2(renvi$Temperature ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
set.seed(910)
permanova_pairwise(x = renvi$Temperature, grp =  renvi$Land.use, permutations = 999, padj = "bonferroni")
#conductiviy
adonis2(renvi$Conductivity ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
#pH
adonis2(renvi$pH ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
#turbidity
adonis2(renvi$Turbidity ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
set.seed(910)
permanova_pairwise(x = renvi$Turbidity, grp =  renvi$Land.use, permutations = 999, padj = "bonferroni")
#inorgN
adonis2(renvi$Inorganic.N ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
#NH4
adonis2(renvi$NH4 ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
#NO3
NO3_data <- na.omit(renvi_a)
NO3_data
adonis2(NO3_data$NO3_1 ~ NO3_data$Land.use, method = "bray", perm =999, padj = "bonferroni")
set.seed(910)
permanova_pairwise(x = NO3_data$NO3_1, grp =  NO3_data$Land.use, permutations = 999, padj = "bonferroni")
#SiO2
adonis2(renvi$Silica ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
#Light
adonis2(renvi$Light ~ renvi$Land.use, method = "bray", perm =999, padj = "bonferroni")
set.seed(910)
permanova_pairwise(x = renvi$Light, grp =  renvi$Land.use, permutations = 999, padj = "bonferroni")