# Install
install.packages("openxlsx")

# LIBRARIES
library(openxlsx) 

# INPUT THE PATH AND FILE NAME OF TARGET XLSX
FilePath <- '~/Desktop/'

# The name of files (i.e. nabc, mcdb, gentry, fia, cbc, bbs, fish and diatom)
FileName <- "diatom"
InputFileType<-".xlsx"
FileID<-paste(FileName, InputFileType, sep = "")

# READ DATA
RawData <- read.xlsx(paste(FilePath, FileID, sep = ""), sheet = 1, colNames = F)

# DETERMINE THE NUMBER OF COWS OF RawData
DataSize <- sapply(RawData, NROW)
GroupStart <- 2
GroupEnd <- 100
GroupNum <-  1

# DEFINE GROUP 
for(i in 3:DataSize[1]-1){
	temp1 = 0
	temp2 = 0
	if (RawData[i,1] == RawData[i+1,1]) temp1 = 1
	if (RawData[i,2] == RawData[i+1,2]) temp2 = 1
	Index = temp1*temp2
	if (Index == 0){
		GroupEnd[GroupNum] = i
		GroupNum = GroupNum+1
		GroupStart[GroupNum] = i+1
	}
}
GroupEnd[GroupNum] = DataSize[1]

# CALCULATION AND OUTPUT

# output = list (RawData[1,1], RawData[1,2], "S", "At", "p", "R2")
for (i in 1:GroupNum){
	A_raw = RawData[GroupStart[i]:GroupEnd[i],4]
	A_raw = as.numeric(as.character(A_raw))
	A=sort(A_raw, decreasing = T)
	S = GroupEnd[i]-GroupStart[i]+1
	temp = c(1:S)
	x = c(1:S)
	y = c(1:S)
	At = sum(A)
	Ninf = 0
	tempp1 = 0
	tempp2 = 0
	for (j in 1:S){
		qr_ = A[j]/A[1]
		Ninf = Ninf + qr_
		pi_ = A[j]/At
		x[j] = log(temp[j])
		y[j] = log(qr_)
		tempp1 = tempp1 + x[j]*y[j]
		tempp2 = tempp2 + x[j]*x[j]
	}
	p = -1*tempp1/tempp2
	sstotal = 0
	ssresid = 0
	my = mean(y)
	for (j in 1:S){
		sy = -1*p*x[j]
		sstotal = sstotal + (y[j]-my)**2
		ssresid = ssresid + (sy-y[j])**2	
	}
	ssreg = sstotal - ssresid
	R2 = ssreg/sstotal
	if (i == 1) {
		output = list (RawData[GroupStart[i],1], RawData[GroupStart[i],2], S, At, p, R2)
		}
	else {
	tempp = list(RawData[GroupStart[i],1], RawData[GroupStart[i],2], S, At, p, R2)
	output = rbind(output,tempp)
	}
}

# Output
OutputFileName = "OutFile - "
OutputFileName = paste(OutputFileName, FileName, sep="")
OutputFileType = ".csv"
OutputFileID = paste(OutputFileName, OutputFileType, sep="")
colnames(output)<-c(RawData[1,1], RawData[1,2], "S", "At", "p", "R2")
write.csv(output, paste(FilePath, OutputFileID, sep=""), row.names=F)