library(groundhog)
set.groundhog.folder("C:\\Groundhog_R\\R4.2.3_2023-04-01")
GroundhogDay <- '2023-04-01'

groundhog.library("dplyr",GroundhogDay)
groundhog.library("ggplot2",GroundhogDay)
groundhog.library("ggrepel",GroundhogDay)
groundhog.library("lubridate",GroundhogDay)
groundhog.library("tibble",GroundhogDay)
groundhog.library("tidyr",GroundhogDay)
groundhog.library("rstatix",GroundhogDay)
groundhog.library("multcompView",GroundhogDay)


setwd("D:\\Google Drive\\0_SpekboomResearchGroup2.0\\3_Experiments\\RegionalTransect21(10)_ParentPlantMaterialExperiment\\manuscript/")
 
read.csv("data_manuscript/parentplantleafmoisturedata_2023-08-29.csv")%>%
  as_tibble()->
  dat_leaves

dat_leaves%>%
  mutate(Site=factor(Site,labels=paste("Site:",1:10)))->
  dat_leaves

# calculating the average of two replicates
dat_leaves%>%
  group_by(Site,Individual)%>%
  summarise(LeafMoisture=mean(LeafMoisture))->
  dat_leaves

# Sites that are significantly not normally distributed
dat_leaves%>%
  group_by(Site)%>%
  shapiro_test(LeafMoisture)%>%
  filter(p<0.06)

# .:. switching to the non-parametric kruskal test
dat_leaves%>%
  as.data.frame()%>%
  rstatix::kruskal_test(LeafMoisture~Site)%>%
  get_test_label(type = "text",detailed = TRUE)

dat_leaves%>%
  as.data.frame()%>%
  kruskal_test(LeafMoisture~Site)%>%
  mutate(text=paste0("H=",round(statistic,1),", df=",df,", p=",p))%>%
  select(text)

# conducting a post-hoc dunn_test.
# https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust
dat_leaves%>%
  as.data.frame()%>%
  dunn_test(LeafMoisture~Site,p.adjust.method = "hochberg")->
  post_hoc

post_hoc$p.adj->ph_v
names(ph_v) <- paste(post_hoc$group1,post_hoc$group2,sep="-")  
cld<- multcompLetters(ph_v)$Letters
Tk<-data.frame(Site=paste0("Site: ",1:10),Letters=cld)

dat_leaves%>%
  group_by(Site,Individual)%>%
  summarise(uLeafMoisture=mean(LeafMoisture))%>%
  ggplot(aes(as.factor(Site),uLeafMoisture))+
  geom_line(colour="darkgrey",size=3)+
  geom_point(colour="black",size=3)+
  geom_text(data = Tk, aes(x = Site, y = 91, label = Letters),fontface = "italic")+
  ylab("Leaf Moisture (%)")+
  xlab("")+
  theme_bw()+
  geom_text_repel(aes(label=Individual))

ggsave("FinalFiguresV2/Fig_2.jpg",width=10/1.5,height=4.5/1.5)