#' FAC-IBM Step 3, Substep A2: Mate acquition
#'
#' @param hab.aq.results.IB Output from individuals-based model
#'
#' @return P.breeding.pair.results.list.IB
#'
#' @export
step3_substepA2_mate_acquire_IB <- function(hab.aq.results.IB){
#create consolidated pairing code
hab.aq.results.IB$pair2 <- NA
hab.aq.results.IB$pair2[which(hab.aq.results.IB$pair == "bc-mg-fg")] <- "cgg"
hab.aq.results.IB$pair2[which(hab.aq.results.IB$pair == "bk-mg-fg")] <- "kgg"
hab.aq.results.IB$pair2[which(hab.aq.results.IB$pair == "bc-mg-fp")] <- "cgp"
hab.aq.results.IB$pair2[which(hab.aq.results.IB$pair == "bk-mg-fp")] <- "kgp"
hab.aq.results.IB$pair2[which(hab.aq.results.IB$pair == "bc-mp-fg")] <- "cpg"
hab.aq.results.IB$pair2[which(hab.aq.results.IB$pair == "bk-mp-fg")] <- "kpg"
hab.aq.results.IB$pair2[which(hab.aq.results.IB$pair == "bc-mp-fp")] <- "cpp"
hab.aq.results.IB$pair2[which(hab.aq.results.IB$pair == "bk-mp-fp")] <- "kpp"
hab.aq.results.IB$pair2 <- factor(hab.aq.results.IB$pair2)
#total number paired
paired.tot.source <- length(grep("^[c]",hab.aq.results.IB$pair2))
paired.tot.sink <- length(grep("^[k]",hab.aq.results.IB$pair2))
N.cgg <- length(which(hab.aq.results.IB$pair2 == "cgg"))
N.kgg <- length(which(hab.aq.results.IB$pair2 == "kgg"))
N.cgp <- length(which(hab.aq.results.IB$pair2 == "cgp"))
N.kgp <- length(which(hab.aq.results.IB$pair2 == "kgp"))
N.cpg <- length(which(hab.aq.results.IB$pair2 == "cpg"))
N.kpg <- length(which(hab.aq.results.IB$pair2 == "kpg"))
N.cpp <- length(which(hab.aq.results.IB$pair2 == "cpp"))
N.kpp <- length(which(hab.aq.results.IB$pair2 == "kpp"))
N.paired.vec <- c(N.cgg,
N.cgp, # g-p
N.cpg,
N.cpp,
N.kgg,
N.kgp, # g- p
N.kpg,
N.kpp)
P.vec.source <- N.paired.vec[1:4]/paired.tot.source
P.vec.sink <- N.paired.vec[5:8]/paired.tot.sink
P.vec.source[is.nan(P.vec.source)] <- 0
P.vec.sink[is.nan(P.vec.sink)] <- 0
P.vec <- c(P.vec.source, P.vec.sink)
P.breeding.pair.results.IB <- c(P.cgg = P.vec[1],
P.cgp = P.vec[2],
P.cpg = P.vec[3] ,
P.cpp = P.vec[4] ,
P.kgg = P.vec[5] ,
P.kgp = P.vec[6] ,
P.kpg = P.vec[7] ,
P.kpp = P.vec[8] )
P.breeding.pair.results.list.IB <- list(P = P.breeding.pair.results.IB,
df = hab.aq.results.IB)
return(P.breeding.pair.results.list.IB)
}
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