## Band Combos
# Determine unused color band combos, export this to Excel, and calculate the number of bands per color needed and cost.

#Updated 6 July 2011

#Install the gregmisc package
library("gregmisc") 

# Create list of all possible band combinations:
bands<-c("AL", "DB", "DG", "K", "LB", "LG", "O", "PI", "R", "V", "W", "Y")
possible.combos<-permutations(12, 4, bands, repeats.allowed=TRUE) #12 refers to number of possible colors. 4 is number of bands a bird can carry.
data.class(possible.combos)
combos.with.AL <- possible.combos[rowSums(possible.combos=="AL") %in% c(1),] #Extract only combos that include one aluminum band.
head(combos.with.AL)
combos.with.AL
NROW(combos.with.AL)

# Create list of unique band combos used:
b=read.csv("yourfilepath/yourfilename.csv", header=TRUE)  #Replace your banding database filename here.
b2=b[b$Species=="SWSP", c("Upper.right",	"Lower.right", "Upper.left",	"Lower.left")] #Select the species you want and the columns containing bands.
b2
NROW(b2)
b3=unique(b2)
b4=as.matrix(b3)

# Remove used combos from possible combo list. Logic supplied by David Winsemius at Heritage Laboratories.
unused.combos=combos.with.AL[apply(combos.with.AL, 1, function(x) max(apply(b4, 1, function(y) all.equal(x, y, check.attributes=FALSE)) ) ) !="TRUE" , ]    # THIS TAKES A WHILE (~3 minutes)! max(c(TRUE,FALSE))==TRUE; cycle through all of 2nd mtx
unused.combos
NROW(unused.combos) 

# Remove combos that include certain colors.  Ex. DG and DB can be confused. LB often looks like W. PI is too bright.                 
combos.without.DG <- unused.combos[rowSums(unused.combos=="DG")==0,]
combos.without.DG.DB <- combos.without.DG[rowSums(combos.without.DG=="DB")==0,]
NROW(combos.without.DG.DB)
combos.without.DG.DB.LB <- combos.without.DG.DB[rowSums(combos.without.DG.DB=="LB")==0,]
NROW(combos.without.DG.DB.LB)
combos.without.DG.DB.LB.PI <- combos.without.DG.DB.LB[rowSums(combos.without.DG.DB.LB=="PI")==0,]
NROW(combos.without.DG.DB.LB.PI)
combos.without.DG.DB.LB.PI

# Subset number of combos that you need.  Here I take the first 250 combos.
new.combos<-combos.without.DG.DB.LB.PI[1:250,] 
new.combos

# Export combos to .csv
colnames(new.combos)=c("Upper.right",	"Lower.right", "Upper.left",	"Lower.left")
write.csv(new.combos, file = "new.combos.csv", row.names = FALSE)
# to read .csv file back into R: read.csv("new.combos.csv")

# Count number of each band needed.
t=table(new.combos[,1:4]) 
t

# Calculate cost of bands (as of Dec. 2009, color bands are $0.25 ea.).
(sum(t)-250)*0.25 # Subtract the 250 AL bands.