#####################################################
##            Examples of data analysis            ##
##      for the materials & methods section        ##
#####################################################

################## PREPARATION #######################

##INSTALLING NECESSATY LIBRARIES (IF NECESSARY)
source("Script/Libraries (Installation).R")

##LOADING NECESSARY LIBARIRES
source("Script/Libraries.R")

##LOADING NECESSARY PROJECT DATA
source("Script/Datasets.R")

##LOADING NECESSARY FUNCTIONS
source("Script/Functions/Examples.R")

#CREATING RESULTS FOLDER (IF NOT ALREADY PRESENT)
dir.create("Output",showWarnings = FALSE)
dir.create("Output/Figures",showWarnings = FALSE)
dir.create("Output/Tables",showWarnings = FALSE)


################# CREATING TABLES #####################
source("Script/Tables/Examples.R")

############# CREATING VISUALISATIONS #################
source("Script/Visualisations/Examples.R")

########### EXAMPLES -  REFERENCES DATA ##################

##TABLE OF EXAMPLES USED (FROM THE REFERENCES DATA)
FinalTable

##PLOTTING RESULTS
#Abundances of said examples
plotExamples1
#Fragmentation of said examples
plotExamples2

##PRINCIPAL COMPONENT ANALYSIS
#Abundances PCA
PCAVisualisation
#Fragmentation PCA
PCAVisualisation2


######## EXAMPLES - METHODS (STATISTICAL) ##############

## EXPLORING DATA - SKARA BRAE NISP
min(DataUsedSkaraBrae$NISP)
mean(DataUsedSkaraBrae$NISP)
median(DataUsedSkaraBrae$NISP)
getmode(DataUsedSkaraBrae$NISP)
max(DataUsedSkaraBrae$NISP)
sd(DataUsedSkaraBrae$NISP)

##VISUALISATION OF SKARA BRAE NISP
plotsNISP1to3

##TESTS
#Shapiro-Wilk Test
shapiro.test(DataUsedSkaraBrae$NISP)
#ANOVA Test
AOVTestResults     <- aov(NISP~as.factor(Location),data=DataUsedSkaraBrae) 
summary(AOVTestResults)
#Levene Test
car::leveneTest(NISP~as.factor(Location),data=DataUsedSkaraBrae, center=mean)
#Kruskall-Wallis Test
kruskal.test(NISP~as.factor(Location),data=DataUsedSkaraBrae)
#Flinger-Killeen Test
fligner.test(NISP~as.factor(Location),data=DataUsedSkaraBrae)

##CORRELATIONS - DATA (SKARA BRAE, NISP TO MNI)
#Simple correlation, coefficient only
cor(DataUsedSkaraBrae$NISP,DataUsedSkaraBrae$MNI, method = "pearson")

#Complex correlation, as a statistical test, with two different methods shown
cor.test(DataUsedSkaraBrae$NISP,DataUsedSkaraBrae$MNI, method = "pearson")
cor.test(DataUsedSkaraBrae$NISP,DataUsedSkaraBrae$MNI, method = "spearman")

##CHI SQARE TEST (SKARA BRAE, NISP to mNI)
chisq.test(DataUsedSkaraBrae[,c(13,16)])

##CORRELATIONS AND CHI SQUARE TEST RESULTS
PatternResults

################# EXPORTING DATA #####################
source("Script/Results/Examples.R")


###########
##  END  ##
###########




