## Supplementary file 14_Comparison of targeted tree sapling heights among treatment groups (Figure 4)

##Load data from "saplingcount data" file (Supplementary file 6)

##Setting sapling height class category
heightclass1<-saplingcount_data[49:72,]  ##10cm to 30cm
heightclass2<-saplingcount_data[1:24,]   ##30cm to 1m
heightclass3<-saplingcount_data[25:48,]  ##1m to 2m
heightclass4<-saplingcount_data[73:96,]  ## >2m 

##Non-parametric analyses per height class
##Treatment effect on sapling height class

##Quercus acuta
kruskal.test(Quercusacuta~Treatment, data = heightclass1)
kruskal.test(Quercusacuta~Treatment, data = heightclass2)
kruskal.test(Quercusacuta~Treatment, data = heightclass3)
kruskal.test(Quercusacuta~Treatment, data = heightclass4)

##Since p-value <0.05 only for height class4 saplings, we perform posthoc test using Dunn's test

##Dunn's test
library(dunn.test)

dunn.test(heightclass4$Quercusacuta,heightclass4$Treatment,method = "bonferroni")


###Abies firma 
kruskal.test(Abiesfirma~Treatment, data = heightclass1)
kruskal.test(Abiesfirma~Treatment, data = heightclass2)
kruskal.test(Abiesfirma~Treatment, data = heightclass3)
##No data available for height class 4 saplings. Thus, test omitted


###Cinnamomum tenuifolium
kruskal.test(Cinnamomumtenuifolium~Treatment, data = heightclass1)
kruskal.test(Cinnamomumtenuifolium~Treatment, data = heightclass2)
kruskal.test(Cinnamomumtenuifolium~Treatment, data = heightclass3)
kruskal.test(Cinnamomumtenuifolium~Treatment, data = heightclass4)

##Only height class 4 saplings showed p-value < 0.05
dunn.test(heightclass4$Cinnamomumtenuifolium,heightclass4$Treatment,method = "bonferroni")


###Castanopsis sieboldii
kruskal.test(Castanopsissieboldii~Treatment, data = heightclass1)
kruskal.test(Castanopsissieboldii~Treatment, data = heightclass2)
kruskal.test(Castanopsissieboldii~Treatment, data = heightclass3)
kruskal.test(Castanopsissieboldii~Treatment, data = heightclass4)

##Only height class 4 saplings showed p-value < 0.05
dunn.test(heightclass4$Castanopsissieboldii,heightclass4$Treatment,method = "bonferroni")

###Eurya japonica
kruskal.test(Euryajaponica~Treatment, data = heightclass1)
kruskal.test(Euryajaponica~Treatment, data = heightclass2)
kruskal.test(Euryajaponica~Treatment, data = heightclass3)
kruskal.test(Euryajaponica~Treatment, data = heightclass4)

##Height class 2,3 and 4 saplings showed p-value < 0.05
dunn.test(heightclass2$Euryajaponica,heightclass2$Treatment,method = "bonferroni")
dunn.test(heightclass3$Euryajaponica,heightclass3$Treatment,method = "bonferroni")
dunn.test(heightclass4$Euryajaponica,heightclass4$Treatment,method = "bonferroni")

###Neolitsea sericea
kruskal.test(Neolitseasericea~Treatment, data = heightclass1)
kruskal.test(Neolitseasericea~Treatment, data = heightclass2)
kruskal.test(Neolitseasericea~Treatment, data = heightclass3)
kruskal.test(Neolitseasericea~Treatment, data = heightclass4)

##Only height class 4 saplings showed p-value < 0.05
dunn.test(heightclass4$Neolitseasericea,heightclass4$Treatment,method = "bonferroni")