utils::globalVariables(c("variable","id.","read.frq","catch","effort","qtr","week","fishery"))
iUMFCL=function(plotFrqFile){
mm=as.data.frame(read.frq(plotFrqFile)$mat[-1,1:6])
mm$effort[mm$effort<0]=NA
mm=transform(mm,index=catch/effort,
month=qtr+week/4,
name =fishery)[,c("name","year","month","qtr","week","index","catch","effort")]
attributes(mm)$smry=mm$fish
return(mm)}
.iUMFCL <-
function(plotrepfile="plot.rep"){
#==============================================================
#
#==============================================================
rtimes <- getrtimes(plotrepfile)
qq <- data.frame(time=sort(unique(unlist(rtimes))))
q <- getCPUEolist(plotrepfile)
for(i in 1:length(q)) qq[[paste("flt",i,sep="")]] <-
q[[i]][match(qq$time,rtimes[[i]])]
qq
}
scanText<-function(string, what = character(0), ...){
## Like scan() but reading from a vector of character strings
tc <- textConnection(string)
result <- scan(tc, what = what, quiet = TRUE, ...)
close(tc)
return(result)}
getplotdat1 <- function(h="",plotrepfile,skip=1) {
##=================================================
## List single line after header h.
##=================================================
dat <- readLines(plotrepfile)
recnum <- grep(h, dat)
scanText(dat[recnum + skip],what=0)
}
getplotdat4 <- function(h="",plotrepfile) {
##=================================================
## Start listing after header h. Quit if encounter
## "^#"
##=================================================
dat <- readLines(plotrepfile)
rec1 <- grep(h, dat)
if(length(rec1) <= 0)
stop(paste('"',h,'"',"not found in",plotrepfile," Die yuppie scum!"))
recnum <- rec1+1
tt <- numeric(0)
for(i in recnum:length(dat)) {
if (regexpr("^#", dat[i]) != -1) break
tt <- c(tt, scanText(dat[i], what = 0))
}
tt
}
"getnfish" <-
function(plotrepfile="plot.rep"){
##==============================================================
## Number of fisheries
##==============================================================
getplotdat1(plotrepfile,h="# Number of fisheries")
}
"getnreal" <-
function(plotrepfile="plot.rep"){
###==============================================================
### Number of realizations per fishery
###==============================================================
getplotdat1(plotrepfile,h="# Number of realizations per fishery")
}
"getrtimes" <-
function(plotrepfile="plot.rep"){
##==============================================================
## Time of each realization by fishery (down)
##==============================================================
dat <- getplotdat4("# Time of each realization by fishery",plotrepfile)
nreal <- getnreal(plotrepfile)
nfish <- getnfish(plotrepfile)
splitter <- rep(seq(nfish), nreal)
split(dat, splitter)
}
"getCPUEolist" <-
function(plotrepfile="plot.rep"){
##==============================================================
## Observed CPUE by fishery (down) and time (across)
##==============================================================
dat <- getplotdat4("# Observed CPUE by fishery",plotrepfile)
nreal <- getnreal(plotrepfile)
nfish <- getnfish(plotrepfile)
splitter <- rep(seq(nfish), nreal)
split(dat, splitter)
}
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