library(ggplot2)
library(ggpubr)
library(ggbiplot)

##Effect of environment variables to snail occurrence and abundance

# Read plant and habitat data file "Additional File 4.csv"
plant_habitat=read.csv(choose.files()) # Select and open Open Additional File 4.csv

# subset habitat data
topygraphy_habitat <- plant_habitat[,c(4:11)]

# PCA analysis
topygraphy_habitat.pca <- prcomp(topygraphy_habitat, center = TRUE,scale. = TRUE)
summary(topygraphy_habitat.pca)
ggbiplot(topygraphy_habitat.pca,choices=c(1,2), labels=plant_habitat[,1], groups = plant_habitat[,2],ellipse=TRUE, labels.size=3, varname.size=3, varname.adjust=1, obs.scale = 1, var.scale = 0)
ggbiplot(topygraphy_habitat.pca,choices=c(2,3), labels=plant_habitat[,1], groups = plant_habitat[,2],ellipse=TRUE, labels.size=3, varname.size=3, varname.adjust=1, obs.scale = 1, var.scale = 0)
ggbiplot(topygraphy_habitat.pca,choices=c(1,3), labels=plant_habitat[,1], groups = plant_habitat[,2],ellipse=TRUE, labels.size=3, varname.size=3, varname.adjust=1, obs.scale = 1, var.scale = 0)



### Microclimatic variables patterns in each plot Figure 4, 5 and 6

## soil temperature
# read data "day-soil summary data July only.csv"
day.soil.summary.data.July.only=read.csv(choose.files()) # Select and Open Additional File 6.csv

summary(day.soil.summary.data.July.only)
tapply(day.soil.summary.data.July.only$Mean.soil.temperature.of.the.day, 
       day.soil.summary.data.July.only$Site, 
       mean)
tapply(day.soil.summary.data.July.only$Maximum.soil.temperature.of.the.day, 
       day.soil.summary.data.July.only$Site, 
       mean)
tapply(day.soil.summary.data.July.only$Mininum.soil.temperature.of.the.day, 
       day.soil.summary.data.July.only$Site, 
       mean)
#create graph
mean_soil<-ggplot(day.soil.summary.data.July.only, aes(Day, Mean.soil.temperature.of.the.day, colour=Site))+labs(title="A")+
  facet_wrap(~Month) +geom_line(size=0.3) + geom_point(size=0.3) + ylim(21,37) + ylab('Mean Soil Temperature')
max_soil<-ggplot(day.soil.summary.data.July.only, aes(Day, Maximum.soil.temperature.of.the.day, colour=Site))+labs(title="B")+
  facet_wrap(~Month) +geom_line(size=0.3) + geom_point(size=0.3) + ylim(21,37) + ylab('Maximum Soil Temperature')
min_soil<-ggplot(day.soil.summary.data.July.only, aes(Day, Mininum.soil.temperature.of.the.day, colour=Site))+labs(title="C")+
  facet_wrap(~Month) +geom_line(size=0.3) + geom_point(size=0.3) + ylim(21,37) + ylab('Minimum Soil Temperature')
#plot graph (6 in X 6 in)
ggarrange(mean_soil,
          max_soil,
          #min_soil,
          ncol = 1, nrow = 2)#nrow = 3)

mean_soil_inset<-ggplot(day.soil.summary.data.July.only, aes(Day, Mean.soil.temperature.of.the.day, colour=Site))+labs(title="A")+
  facet_wrap(~Month) +geom_line(size=0.3)+ geom_line(aes(linetype=Site, colour=Site))  + geom_point(size=0.3) +
  scale_color_manual(values=c("blue","red","grey60","grey60","grey60","grey60")) +
  ylim(21,37) + ylab('Mean Soil Temperature')
max_soil_inset <-ggplot(day.soil.summary.data.July.only, aes(Day, Maximum.soil.temperature.of.the.day, colour=Site))+labs(title="B")+
  facet_wrap(~Month) +geom_line(size=0.3)+ geom_line(aes(linetype=Site, colour=Site))  + geom_point(size=0.3) +
  scale_color_manual(values=c("blue","red","grey60","grey60","grey60","grey60")) +
  ylim(21,37) + ylab('Maximum Soil Temperature')
#plot graph (6 in X 6 in) Inset
ggarrange(mean_soil_inset,
          max_soil_inset,
          #min_soil,
          ncol = 1, nrow = 2)#nrow = 3)


## temperature
# read data "day-temp summary data July only.csv"
day.temp.summary.data.July.only =read.csv(choose.files()) # Select and Open Additional File 6.csv
#summary
summary(day.temp.summary.data.July.only)
tapply(day.temp.summary.data.July.only$Mean.air.temperature.of.the.day, 
       day.temp.summary.data.July.only$Site, 
       mean)
tapply(day.temp.summary.data.July.only$Maximum.air.temperature.of.the.day, 
       day.temp.summary.data.July.only$Site, 
       mean)
tapply(day.temp.summary.data.July.only$Mininum.air.temperature.of.the.day, 
       day.temp.summary.data.July.only$Site, 
       mean)
#create graph
mean_temp<-ggplot(day.temp.summary.data.July.only, aes(Day, Mean.air.temperature.of.the.day, colour=Site))+labs(title="A")+
  facet_wrap(~Month) +geom_line(size=0.3) + geom_point(size=0.3) + ylim(21,37) + ylab('Mean Air Temperature')
max_temp<-ggplot(day.temp.summary.data.July.only, aes(Day, Maximum.air.temperature.of.the.day, colour=Site))+labs(title="B")+
  facet_wrap(~Month) +geom_line(size=0.3) + geom_point(size=0.3) + ylim(21,37) + ylab('Maximum Air Temperature')
min_temp<-ggplot(day.temp.summary.data.July.only, aes(Day, Mininum.air.temperature.of.the.day, colour=Site))+labs(title="C")+
  facet_wrap(~Month) +geom_line(size=0.2) + geom_point(size=0.3) + ylim(21,37) + ylab('Minimum Air Temperature')
#plot graph (6 in X 6 in)
ggarrange(mean_temp,
          max_temp,
          #min_temp,
          ncol = 1, nrow = 2)#nrow = 3)

mean_temp_inset<-ggplot(day.temp.summary.data.July.only, aes(Day, Mean.air.temperature.of.the.day, colour=Site))+labs(title="A")+
  facet_wrap(~Month) +geom_line(size=0.3)+ geom_line(aes(linetype=Site, colour=Site)) + geom_point(size=0.3) + 
  scale_color_manual(values=c("blue","red","grey60","grey60","grey60","grey60","grey60","grey60")) +
  ylim(21,37) + ylab('Mean Air Temperature')
max_temp_inset<-ggplot(day.temp.summary.data.July.only, aes(Day, Maximum.air.temperature.of.the.day, colour=Site))+labs(title="B")+
  facet_wrap(~Month) +geom_line(size=0.3)+ geom_line(aes(linetype=Site, colour=Site)) + geom_point(size=0.3) + 
  scale_color_manual(values=c("blue","red","grey60","grey60","grey60","grey60","grey60","grey60")) +
  ylim(21,37) + ylab('Maximum Air Temperature')
#plot graph (6 in X 6 in) inset
ggarrange(mean_temp_inset,
          max_temp_inset,
          #min_temp,
          ncol = 1, nrow = 2)#nrow = 3)


## Humidity
# read data "day-humid summary data July only.csv"
day.humid.summary.data.July.only=read.csv(choose.files()) # Select and Open Additional File 6.csv
#summary
summary(day.humid.summary.data.July.only)
tapply(day.humid.summary.data.July.only$Mean.relative.humidity.of.the.day, 
       day.humid.summary.data.July.only$Site, 
       mean)
tapply(day.humid.summary.data.July.only$Maximum.relative.humidity.of.the.day, 
       day.humid.summary.data.July.only$Site, 
       mean)
tapply(day.humid.summary.data.July.only$Mininum.relative.humidity.of.the.day, 
       day.humid.summary.data.July.only$Site, 
       mean)
#create graph
mean_hum<-ggplot(day.humid.summary.data.July.only, aes(Day, Mean.relative.humidity.of.the.day, colour=Site))+labs(title="A")+
  facet_wrap(~Month) +geom_line(size=0.3) + geom_point(size=0.3) + ylim(30,100) + ylab('Mean Air Humidity') 
max_hum<-ggplot(day.humid.summary.data.July.only, aes(Day, Maximum.relative.humidity.of.the.day, colour=Site))+labs(title="B")+
  facet_wrap(~Month) +geom_line(size=0.3) + geom_point(size=0.3) + ylim(30,100) + ylab('Maximum Air Humidity')
min_hum<-ggplot(day.humid.summary.data.July.only, aes(Day, Mininum.relative.humidity.of.the.day, colour=Site))+#labs(title="C")+
  facet_wrap(~Month) +geom_line(size=0.3) + geom_point(size=0.3) + ylim(30,100) + ylab('Minimum Air Humidity')
#plot graph (6 in X 6 in)
ggarrange(mean_hum,
          max_hum,
          #min_hum,
          ncol = 1, nrow = 2)#nrow = 3)

mean_hum_inset<-ggplot(day.humid.summary.data.July.only, aes(Day, Mean.relative.humidity.of.the.day, colour=Site))+labs(title="A")+
  facet_wrap(~Month) +geom_line(size=0.3)+ geom_line(aes(linetype=Site, colour=Site))  + geom_point(size=0.3) + 
  scale_color_manual(values=c("blue","grey60","grey60","grey60","grey60","grey60","grey60","grey60")) +
  ylim(30,100) + ylab('Mean Air Humidity')
max_hum_inset<-ggplot(day.humid.summary.data.July.only, aes(Day, Maximum.relative.humidity.of.the.day, colour=Site))+labs(title="B")+
  facet_wrap(~Month) +geom_line(size=0.3)+ geom_line(aes(linetype=Site, colour=Site))  + geom_point(size=0.3) + 
  scale_color_manual(values=c("blue","grey60","grey60","grey60","grey60","grey60","grey60","grey60")) +
  ylim(30,100) + ylab('Maximum Air Humidity')
#plot graph (6 in X 6 in) inset
ggarrange(mean_hum_inset,
          max_hum_inset,
          #min_hum,
          ncol = 1, nrow = 2)#nrow = 3)


## temperature, Humidity, soil temperature of different time of days
# read data "Climate time 2hr of the date.csv"
time.temp.humid.doil.summary.data.July.only =read.csv(choose.files()) # Select and Open Additional File 6.csv
#create graph
mean_soil_time <-ggplot(time.temp.humid.doil.summary.data.July.only, aes(Time.of.the.Day, Mean.Soil.Temperature....C., colour=Plots))+labs(title="A")+
  geom_point(size=0.75) + ylim(21,37) + ylab('Mean Soil Temperature')+ 
  theme(axis.ticks.x = element_blank(), axis.text.x = element_blank(),axis.title.x=element_blank())
mean_temp_time <-ggplot(time.temp.humid.doil.summary.data.July.only, aes(Time.of.the.Day, Mean.Air.Temperature...C., colour=Plots))+labs(title="B")+
  geom_point(size=0.75) + ylim(21,37) + ylab('Mean Air Temperature') + 
  theme(axis.ticks.x = element_blank(), axis.text.x = element_blank(),axis.title.x=element_blank())
mean_hum_time <-ggplot(time.temp.humid.doil.summary.data.July.only, aes(Time.of.the.Day, Mean.Air.Humidity...., colour=Plots))+labs(title="C")+
  geom_point(size=0.75) + ylim(30,100) + ylab('Mean Air Humidity')+ 
  theme(axis.ticks.x = element_blank(), axis.text.x = element_blank(),axis.title.x=element_blank())

X_axis_lab <-ggplot(time.temp.humid.doil.summary.data.July.only, aes(Time.of.the.Day, Mean.Soil.Temperature....C., colour=Plots))+labs(title="C")+
  geom_point(size=0.5) + ylim(21,37) + ylab('Mean Soil Temperature')+ xlab('Time of the Day') + theme(axis.text.x = element_text(angle=30, hjust=1))

#plot graph (8 in X 6 in)
ggarrange(mean_soil_time,
          mean_temp_time,
          mean_hum_time,
          #min_temp,
          ncol = 1, nrow = 3)



## The correlation between the abundance of snails and the 4 plant species.
# Read plant and habitat data file "Additional File 4.csv"
snail_plant_habitat=read.csv(choose.files()) # Select and open Open Additional File 4.csv

# subset snail data and the 4 plant species data
snail_4_plants <- snail_plant_habitat[,c(3,15,16,22,30)]

par(mfrow=c(2,2))
plot(snail_4_plants$Kibatalia.laurifolia,snail_4_plants$No.of.living.snails, 
     xlab = expression(italic("Kibatalia laurifolia ") (abundance)),ylab=expression(italic("Pollicaria elephas ") (abundance)),
     pch = 16, col="grey1", xlim=c(0,8))

plot(snail_4_plants$Croton.cascarilloides,snail_4_plants$No.of.living.snails, 
     xlab = expression(italic("Croton cascarilloides ") (abundance)),ylab=expression(italic("Pollicaria elephas ") (abundance)),
     pch = 16, col="grey1", xlim=c(0,8))

plot(snail_4_plants$Mallotus.peltatus,snail_4_plants$No.of.living.snails, 
     xlab = expression(italic("Mallotus peltatus ") (abundance)),ylab=expression(italic("Pollicaria elephas ") (abundance)),
     pch = 16, col="grey1", xlim=c(0,8))

plot(snail_4_plants$Diospyros.toposia.var..toposoides,snail_4_plants$No.of.living.snails, 
     xlab = expression(italic("Diospyros toposia")~"var"~italic("toposoides ")~(abundance)),ylab=expression(italic("Pollicaria elephas ") (abundance)),
     pch = 16, col="grey1", xlim=c(0,8))