RFunctions

##-------Some basic function work with datasets in R----------
##-------NOTE: You need Owls.txt to run this file-------------


#Function to calculate missing values per variable
NAPerVariable <- function(X1) {
  D1 <- is.na(X1)
	colSums (D1)
}

#Function to calculate 0 values per variable
ZerosPerVariable <- function(X1) {
	D1 <- (X1 == 0)
	colSums (D1)
}

#Combining them into one, and warning if a typo is made:
VariableInfo <- function(X1, Choice1) {
	if (Choice1 == "Zeros") {D1 = (X1 == 0) }
	if (Choice1 == "NAs") {D1 <- is.na(X1) }
	if (Choice1 != "Zeros" & Choice1 != "NAs") {
		print("You made a typo")} else {
	colSums (D1, na.rm = TRUE)}
}

#using ifelse
VariableInfo <- function(X1, Choice1) {
	ifelse (Choice1 == "Zeros", D1 <- (X1 == 0),
								 D1 <- is.na(X1))
	if (Choice1 != "Zeros" & Choice1 != "NAs") {
		print("You made a typo")} else {
	colSums (D1, na.rm = TRUE)}
}

#--------------------------------------------------------------------------------------------------------------------------------------

#--Pseudocode
# Import Data
# Make variable names for generic Nest/FoodTreatment Data
# Make a function with the input of nest and foodtreatment
#Output data
Owls <- read.table("Owls.txt", header = TRUE)
AllNests <- unique(Owls$Nest)
AllFT <- unique(Owls$FoodTreatement)

NestFood <- function(X1, Choice1, Choice2) {
	NestName = Choice1
	FT = Choice2
	ifelse (Choice1 == NestName & Choice2 == "Satiated", 
							D1 <- X1[X1$Nest == NestName 														  		& X1$FoodTreatment == "Satiated",],
							D1 <- X1[X1$Nest == NestName 
							& X1$FoodTreatment == "Deprived",])
	if (Choice2 != "Satiated" & Choice2 != "Deprived") {
		print("You made a typo")} else {
	  	plot (x = D1$ArrivalTime,
	  	y = D1$NegPerChick, xlab = "Arrival Time",
	  	ylab = "Negotation Behavior", main = paste(NestName,FT,sep = " - "))
	  	print(D1)
			}
}

#--------------------------------------------------------------------------------------------------------------------------------------
Benthic <- read.table("RIKZ.txt", header = TRUE)
Species <- Benthic[,2:76]
n <- dim(Species)
n

#Total abundance per site
TA <- rowSums(Species, na.rm = TRUE)
Richness <- rowSums(Species > 0, na.rm = TRUE)
prop <- Species/TA
H <- -rowSums(prop*log10(prop), na.rm = TRUE)
H

Index.function <- function(Spec, Choice1) {
if (Choice1 == "Richness") {
	Index <- rowSums(Species > 0, na.rm = TRUE) }
if (Choice1 == "Total Abundance") {
	Index <- rowSums(Species, na.rm = TRUE) }
if (Choice1 == "Shannon") {
	RS <- rowSums(Species, na.rm = TRUE)
	prop <- Species/TA
	Index <- -rowSums(prop*log10(prop), na.rm = TRUE) } else {
		print("Check your choice")
		Index <- NA }
	
	list(Index = Index, MyChoice = Choice1)
}