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("cmartin/ggConvexHull",GroundhogDay)
groundhog.library("ggpmisc",GroundhogDay)



setwd("D:\\Google Drive\\0_SpekboomResearchGroup2.0\\3_Experiments\\RegionalTransect21(10)_ParentPlantMaterialExperiment\\manuscript/")

read.csv("data_manuscript/harvestdata_2023-08-29.csv")%>%
  as_tibble()->
  dat_all

read.csv("data_manuscript/parentplantleafmoisturedata_2023-08-29.csv")%>%
  as_tibble()->
  dat_pp

read.csv("data_manuscript/harvest_days.csv")%>%
  as_tibble()->
  harvestdates


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

dat_all%>%
  filter(SamplingEvent%in%c(4,5,6,7,8))%>%
  group_by(SamplingEvent,Site,Individual)%>%
  summarise(uRootMass=mean(RootMass,na.rm=T),
            uLeafMoisture=mean(LeafMoisture,na.rm=T))%>%
  filter(!is.na(uRootMass))%>%
  filter(!is.na(uLeafMoisture))%>%
  left_join(harvestdates)%>%
  left_join(
    dplyr::select(dat_pp,Site,Individual,LeafMoisture)%>%
      group_by(Site,Individual)%>%
      summarise(LeafMoisture=mean(LeafMoisture)))%>%
  mutate(DaysSincePlanting=factor(DaysSincePlanting,levels=c(35,42,48,56,103),
                                  labels=c("35 days","42 days","48 days","56 days","103 days")))->
  forGG
forGG%>%
  ungroup()%>%
  select(Site,Individual,LeafMoisture,uRootMass,DaysSincePlanting)%>%
  group_by(Individual,Site,DaysSincePlanting)%>%
  summarise(LeafMoisture=mean(LeafMoisture),
            uRootMass=mean(uRootMass))%>%
  slice(chull(LeafMoisture,uRootMass))->
  forGGhull

forGG%>%
  group_by(Site,DaysSincePlanting)%>%
  summarise(LeafMoisture=mean(LeafMoisture),
            uRootMass=mean(uRootMass))%>%
  mutate(label=gsub("Site: ","",Site))->
  forGG_sitelabels

forGG%>%
  mutate(plant_label=paste(gsub("Site: ","",Site),":",LETTERS[Individual],sep=""))%>%
  ggplot(aes(LeafMoisture,uRootMass))+
  stat_poly_line() +
  stat_poly_eq(use_label(c("F","R2","P"),sep="*\"; \"*"),small.r=TRUE,small.p=TRUE)+
  
  geom_convexhull(alpha = 0.3, aes(fill = Site,group=Site))+
  geom_point(aes(colour=Site,group=Site))+
  geom_text_repel(data=forGG_sitelabels,aes(x=LeafMoisture,y=uRootMass,label=label,colour=Site),
                 min.segment.length = 0, seed = 42, box.padding = 0.5)+
  facet_wrap(~DaysSincePlanting,ncol=2)+
  xlab("Leaf moisture (%) of parent plant at time of harvesting")+
  ylab("Dry root mass (g)")+
  theme(legend.position="none")+
  scale_y_continuous(expand = c(0, 0), limits = c(-0.05, NA))
  
ggsave(paste("FinalFiguresV2/Fig_S4.jpg",sep=""),width=7,height=9)