setwd("D://DESARROLLO DEL PROYECTO/ARTICULOS DEL PROYECTO/AVES/DIVERSIDAD/ANALISIS_AVES/ANALISIS R/DIVERSIDAD_AMBIENTALES")

Polylepis <- read.csv("Datos_Completos.csv",";",header = T)
Polylepis
head(Polylepis)
library(ggplot2)
library(plotly)
require(corrgram)
require(ggplot2)
require(lme4)
require(cowplot)
library(plotly)
library(ggthemes)
library(gridExtra)
library(grid)
library(lattice)
require(stats) 
require(multcompView)
require(dunn.test)
require(FSA)
require(PMCMR)
require(ggplot2)

####box plot de altura de los arbolews de Polylepis junin
###Analisis de Kruskal wallis
Polylepis <- read.csv("Datos_Completos.csv",";",header = T)
head(Polylepis)
tail(Polylepis)
attach(Polylepis)
names(Polylepis)
tapply(Polylepis$TH, Polylepis$Locality, median,na.rm=TRUE)
kruskal.test(TH~Locality, data=Polylepis)
out <- posthoc.kruskal.dunn.test(TH ~ Locality,data = Polylepis, p.adjust="bonf")
summary(out)
out
out.p <- get.pvalues(out)
out.mcV <- multcompLetters(out.p, threshold=0.01)
out.mcV
#### Altura de los arboles de polylepis
TH<- ggplot(Polylepis, aes(x=reorder(Locality,TH), y=TH, fill=interaction(Species,Locality), dodge=Species))+
  stat_boxplot(geom = "errorbar", width = 0.35)+ geom_boxplot(position=position_dodge(width=0.8))+
   theme_classic()+  theme(axis.text.x = element_text(face="bold",color="black", size=11, angle=0),
                         axis.text.y = element_text(face="bold", color="black", 
                                                    size=9, angle=0))+ scale_fill_manual(values=c("gray60","gray30","gray30","gray30",
                                                                                                   "gray90","gray90","gray60","gray30"))+xlab("Locality") +
  ylab("height of trees per 10x10 m plot (m)")+scale_y_continuous(breaks = c(1,3,5,7,9,11,13,15))+
  theme(axis.text=element_text(size=8),axis.title=element_text(size=12,face="bold"))+
  theme(legend.position = "bottom", legend.direction = "horizontal")+
  annotate("text", x = "Qui", y = 7, label = "a",parse = TRUE,size=6)+
  annotate("text", x = "Cha", y = 9.5, label = "b",parse = TRUE,size=6)+
  annotate("text", x = "Pau", y = 9.5, label = "b",parse = TRUE,size=6)+
  annotate("text", x = "Sha", y = 12, label = "c",parse = TRUE,size=6)+
  annotate("text", x = "Juc", y = 14.5, label = "d",parse = TRUE,size=6)+
  annotate("text", x = "Lla", y = 14.5, label = "d",parse = TRUE,size=6)+
  annotate("text", x = "Nah", y = 15.3, label = "de",parse = TRUE,size=6)+
  annotate("text", x = "Tas", y = 14, label = "e",parse = TRUE,size=6)+
  theme(legend.title=element_blank())
TH

#+ stat_boxplot(geom ='errorbar')
#### Diametro de los arboles de polylepis
tapply(Polylepis$DGL, Polylepis$Locality, median,na.rm=TRUE)
kruskal.test(DGL~Locality, data=Polylepis)
out <- posthoc.kruskal.dunn.test(DGL ~ Locality,data = Polylepis, p.adjust="bonf")
summary(out)
out
out.p <- get.pvalues(out)
out.mcV <- multcompLetters(out.p, threshold=0.01)
out.mcV

DGL<-ggplot(Polylepis, aes(x=reorder(Locality,DGL),y=DGL, fill=interaction(Species,Locality), dodge=Species))+
  stat_boxplot(geom = "errorbar", width = 0.35)+ geom_boxplot(position=position_dodge(width=0.8))+
  theme_classic()+ theme(axis.text.x = element_text(face="bold",color="black", size=11, angle=0),
                         axis.text.y = element_text(face="bold", color="black", 
                                                    size=9, angle=0))+ scale_fill_manual(values=c("gray60","gray30","gray30","gray30",
                                                                                                   "gray90","gray90","gray60","gray30"))+xlab("Locality") +
  ylab("dgl of trees per 10x10 m plot (m)")+scale_y_continuous(breaks = c(10,20,30,40,50,60,70))+
  theme(axis.text=element_text(size=8),axis.title=element_text(size=12,face="bold"))+
  theme(legend.position = "bottom", legend.direction = "horizontal")+
  annotate("text", x = "Qui", y = 35, label = "a",parse = TRUE,size=6)+
  annotate("text", x = "Pau", y = 35, label = "a",parse = TRUE,size=6)+
  annotate("text", x = "Cha", y = 40, label = "b",parse = TRUE,size=6)+
  annotate("text", x = "Sha", y = 40, label = "b",parse = TRUE,size=6)+
  annotate("text", x = "Lla", y = 40, label = "b",parse = TRUE,size=6)+
  annotate("text", x = "Juc", y = 40, label = "b",parse = TRUE,size=6)+
  annotate("text", x = "Nah", y = 59, label = "c",parse = TRUE,size=6)+
  annotate("text", x = "Tas", y = 72, label = "d",parse = TRUE,size=6)+
  theme(legend.title=element_blank())
DGL


Figure_3<- plot_grid(TH,DGL, labels = c("",""), align="v", axis="l",rel_widths = c(1,1), nrow = 1,ncol=2)
Figure_3
###save the figure in 800 dpi, format jpg
ggsave(Figure_3,width=12, height=4, file="Figure 3.jpg", dpi = 800)