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flop_msfd.control.r
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flop_msfd.control.r
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### class ######################################################################
validFLOP.MSFD.control <- function(object){
if ( !(object@do.community.biomass.demersal %in% c(0,1))) return("option do.community.biomass.demersal must have the value 0 or 1")
# Everything is fine
return(TRUE)
}
setClass("FLOP.MSFD.control",
representation(
do.community.biomass.demersal ="numeric",
community.biomass.demersal.ages="matrix",
do.community.biomass.small ="numeric",
community.biomass.small.ages="matrix",
do.community.biomass.pelagic ="numeric",
community.biomass.pelagic.ages="matrix",
do.community.biomass.forage ="numeric",
community.biomass.forage.ages="matrix",
do.M2.bar ="numeric",
M2.bar.ages ="matrix",
do.mean.weight.at.age ="numeric",
mean.weight.at.age.sp ="matrix",
do.community.mean.weight ="numeric",
community.mean.weight.sp ="matrix",
do.mean.weight.C ="numeric",
mean.weight.C.sp ="matrix",
do.community.mean.weight.C ="numeric",
community.mean.weight.C.sp ="matrix",
do.community.F ="numeric",
community.F.sp ="matrix",
do.community.M ="numeric",
community.M.sp ="matrix",
do.life.expectancy ="numeric",
life.expectancy.first.age ="matrix",
do.community.life.expectancy ="numeric",
community.life.expectancy.options="matrix",
do.size.spectra ="numeric",
size.spectra.sp ="matrix",
do.LFI ="numeric",
LFI.sp ="matrix",
LFI.age ="matrix"
)
,
prototype=prototype(
do.community.biomass.demersal =0,
community.biomass.demersal.ages =matrix(0,ncol=1,nrow=2,dimnames=list(c("first.age","last.age"),c("sp1"))),
do.M2.bar =0,
M2.bar.ages =matrix(0,ncol=1,nrow=2,dimnames=list(c("first.age","last.age"),c("sp1"))),
do.mean.weight.at.age =0,
mean.weight.at.age.sp =matrix(1,ncol=1,nrow=1,dimnames=list(c("include"),c("sp1"))),
do.community.mean.weight =0,
community.mean.weight.sp =matrix(1,ncol=1,nrow=1,dimnames=list(c("include"),c("sp1"))),
do.mean.weight.C =0,
mean.weight.C.sp =matrix(1,ncol=1,nrow=1,dimnames=list(c("include"),c("sp1"))),
do.community.mean.weight.C =0,
community.mean.weight.C.sp =matrix(1,ncol=1,nrow=1,dimnames=list(c("include"),c("sp1"))),
do.community.F =0,
community.F.sp =matrix(1,ncol=1,nrow=1,dimnames=list(c("include"),c("sp1"))),
do.community.M =0,
community.M.sp =matrix(1,ncol=1,nrow=1,dimnames=list(c("include"),c("sp1"))),
do.life.expectancy =0,
life.expectancy.first.age =matrix(1,ncol=1,nrow=1,dimnames=list(c("first.age"),c("sp1"))),
do.community.life.expectancy =0,
community.life.expectancy.options=matrix(1,ncol=1,nrow=2,dimnames=list(c("first.age","weighting"),c("sp1"))),
do.size.spectra =0,
size.spectra.sp =matrix(1,ncol=1,nrow=1,dimnames=list(c("include"),c("sp1"))),
do.LFI =0,
LFI.sp =matrix(1,ncol=1,nrow=1,dimnames=list(c("include"),c("sp1"))),
LFI.age =matrix(1,ncol=1,nrow=1,dimnames=list(c("first.age"),c("sp1"))),
do.community.biomass.small =0,
community.biomass.small.ages=matrix(0,ncol=1,nrow=2,dimnames=list(c("first.age","last.age"),c("sp1"))),
do.community.biomass.pelagic =0,
community.biomass.pelagic.ages=matrix(0,ncol=1,nrow=2,dimnames=list(c("first.age","last.age"),c("sp1"))),
do.community.biomass.forage =0,
community.biomass.forage.ages=matrix(0,ncol=1,nrow=2,dimnames=list(c("first.age","last.age"),c("sp1")))
)
,
validity=validFLOP.MSFD.control
)
setValidity("FLOP.MSFD.control", validFLOP.MSFD.control)
# in final version remove(validOP.control) # We do not need this function any more
### End class ###########################################################
### Methods #############################################################
FLOP.MSFD.control <- function()
{
Init.function()
VPA.species.names<-sp.names[first.VPA:nsp]
all.species.names<-sp.names[1:nsp]
no.species<-nsp-first.VPA+1
fala<-matrix(c(rep(fa,no.species),SMS.control@species.info[first.VPA:nsp,'last-age']),byrow=T,ncol=no.species,nrow=2,dimnames=list(c("first.age","last.age"),VPA.species.names))
fala2<-matrix(c(rep(fa,no.species),SMS.control@species.info[first.VPA:nsp,'last-age']),byrow=T,ncol=no.species,nrow=2,dimnames=list(c("first.age","weighting"),VPA.species.names))
fala.all<-matrix(c(rep(fa,nsp),SMS.control@species.info[1:nsp,'last-age']),byrow=T,ncol=nsp,nrow=2,dimnames=list(c("first.age","last.age"),all.species.names))
inclsp<-matrix(1,ncol=no.species,nrow=1,dimnames=list(c("include"),VPA.species.names))
inclsp.all<-matrix(1,ncol=nsp,nrow=1,dimnames=list(c("include"),all.species.names))
res <- new("FLOP.MSFD.control",
do.community.biomass.demersal =as.integer(0),
community.biomass.demersal.ages =fala.all,
do.M2.bar =as.integer(0),
M2.bar.ages =fala,
do.mean.weight.at.age =as.integer(0),
mean.weight.at.age.sp =inclsp,
do.community.mean.weight =as.integer(0),
community.mean.weight.sp =inclsp,
do.mean.weight.C =as.integer(0),
mean.weight.C.sp =inclsp,
do.community.mean.weight.C =as.integer(0),
community.mean.weight.C.sp =inclsp,
do.community.F =as.integer(0),
community.F.sp =inclsp,
do.community.M =as.integer(0),
community.M.sp =inclsp,
do.life.expectancy =as.integer(0),
life.expectancy.first.age =inclsp,
do.community.life.expectancy =as.integer(0),
community.life.expectancy.options=fala2,
do.size.spectra =as.integer(0),
size.spectra.sp =inclsp.all,
do.LFI =as.integer(0),
LFI.sp =inclsp.all,
LFI.age =inclsp.all,
do.community.biomass.small =as.integer(0),
community.biomass.small.ages =fala.all,
do.community.biomass.pelagic =as.integer(0),
community.biomass.pelagic.ages=fala.all,
do.community.biomass.forage =as.integer(0),
community.biomass.forage.ages =fala.all)
return(res)
}
###
###
write.FLOP.MSFD.control<-function(control,file="op_msfd.dat",path=NULL,nice=TRUE,writeSpNames=T) {
wr.matrix<-function(m,text){
cat("# ",text,"\n",file=file,append=TRUE)
for (j in (1:dim(m)[1])) cat(m[j,],"\n",file=file,append=TRUE)
}
wr.matrix.nice<-function(m,sp){
cat("#",formatC(sp,width=11),"\n",file=file,append=TRUE)
for (j in (1:dim(m)[1])) cat(formatC(m[j,],width=11),"\n",file=file,append=TRUE)
}
if (!inherits(control, "FLOP.MSFD.control"))
stop(paste("control" ,"must be an 'FLOP.MSFD.contol' object!"))
old.path<-getwd()
if (!is.null(path)) setwd(path)
sepLine<-"########################################\n"
sp.names<-dimnames(slot(control,"community.biomass.demersal.ages"))[[2]]
VPA.sp.names<-sp.names[first.VPA:nsp]
cat("# options for calculation of MSFD and other indicatores\n",file=file)
cat('# the character "#" is used as comment character, such that all text and numbers after # are skipped\n#\n',file=file, append=TRUE)
n.<-slotNames(control)
for (x in n.) {
switch(x,
"do.community.biomass.demersal" ={if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate Biomass of demersal fish (option do.community.biomass.demersal)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.biomass.demersal.ages" ={if (nice) {
cat("# First and last ages to be used for calc of demersal fish biomass. Negative value excludes the species\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.M2.bar" ={if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate average M2 by species (option do.M2.bar)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"M2.bar.ages" ={if (nice) {
cat("# First and last ages to be used for calc of mean M2, Negative value excludes the species\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.mean.weight.at.age" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate mean weight at age in the sea (option do.mean.weight.at.age)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"mean.weight.at.age.sp" ={if (nice) {
cat("# Include species 0=no, 1=yes\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.community.mean.weight" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate mean weight in the sea for the whole comunity (option do.community.mean.weight)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.mean.weight.sp" ={if (nice) {
cat("# Include species 0=no, 1=yes\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.mean.weight.C" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate mean weight in the catch (option do.mean.weight.C)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"mean.weight.C.sp" ={if (nice) {
cat("# Include species 0=no, 1=yes\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.community.mean.weight.C" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate mean weight in the catch for the whole comunity (option do.community.mean.weight.C)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.mean.weight.C.sp" ={if (nice) {
cat("# Include species 0=no, 1=yes\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.community.F" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate catch biomass/ stock biomass ratio (option do.community.F)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.F.sp" ={if (nice) {
cat("# Include species 0=no, 1=yes\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.community.M" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate dead (M) biomass/ stock biomass ratio (option do.community.M)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.M.sp" ={if (nice) {
cat("# Include species 0=no, 1=yes\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.life.expectancy" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate life expectancy (option do.life.expectancy)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"life.expectancy.first.age" ={if (nice) {
cat("# First age used. Negative means not used\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.community.life.expectancy" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate community life expectancy (option do.community.life.expectancy)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.life.expectancy.options" ={if (nice) {
cat("# First age used. Negative means not used\n",file=file,append=T,sep="")
cat("# Weighting factor, positve=input value, -1=recruitment \n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),VPA.sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.size.spectra" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate Size spectrum slope and intercept (option do.size.spectra)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"size.spectra.sp" ={if (nice) {
cat("# Include species 0=no, 1=yes\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.LFI" = {if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate Large Fish Indicator (option do.LFI)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"LFI.sp" ={if (nice) {
cat("# LFI, include species in LFI (0=no, 1=yes)\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),sp.names)
} else wr.matrix(slot(control,x),x)
},
"LFI.age" ={if (nice) {
cat("# LFI, first age considerd as a Large Fish\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.community.biomass.small" ={if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate Biomass of small fish (option do.community.biomass.small)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.biomass.small.ages" ={if (nice) {
cat("# First and last ages to be used for calc of small fish biomass. Negative value excludes the species\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.community.biomass.pelagic" ={if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate Biomass of pelagic fish (option do.community.biomass.pelagic)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.biomass.pelagic.ages" ={if (nice) {
cat("# First and last ages to be used for calc of pelagic fish biomass. Negative value excludes the species\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),sp.names)
} else wr.matrix(slot(control,x),x)
},
"do.community.biomass.forage" ={if (nice) {
cat(sepLine,file=file,append=T)
cat("## Calculate Biomass of forage fish (option do.community.biomass.forage)\n# 0=no, 1=yes\n",
slot(control,x),"\n",file=file,append=T,sep="")
} else cat(slot(control,x),"\t#",x,"\n",file=file,append=TRUE)
},
"community.biomass.forage.ages" ={if (nice) {
cat("# First and last ages to be used for calc of forage fish biomass. Negative value excludes the species\n",file=file,append=T,sep="")
wr.matrix.nice(slot(control,x),sp.names)
} else wr.matrix(slot(control,x),x)
}
) #end switch
}
setwd(old.path)
}
#####
read.FLOP.MSFD.control<-function(file="op_msfd.dat",n.VPA,n.other.pred) {
n.sp<-n.VPA+n.other.pred
species.names<-readLines("species_names.in", n=n.sp)
species.names<-species.names[(n.other.pred+1):n.sp]
species.names<-gsub('_',' ',species.names)
species.names<-sub('[[:space:]]+$', '', species.names)
all.species.names<-readLines("species_names.in", n=n.sp)
all.species.names<-all.species.names[1:n.sp]
all.species.names<-gsub('_',' ',all.species.names)
all.species.names<-sub('[[:space:]]+$', '', all.species.names)
opt<-scan(file, comment.char = "#",quiet=TRUE)
n<-1
control<-new("FLOP.MSFD.control")
n.<-slotNames(control)
for (x in n.) {
switch(x,
"community.biomass.demersal.ages" = {slot(control,x)<-matrix(opt[n:(n-1+2*n.sp)],ncol=n.sp,nrow=2,dimnames=list(c("first.age","last.age"),all.species.names),byrow=TRUE); n<-n+2*n.sp},
"M2.bar.ages" = {slot(control,x)<-matrix(opt[n:(n-1+2*n.VPA)],ncol=n.VPA,nrow=2,dimnames=list(c("first.age","last.age"),species.names),byrow=TRUE); n<-n+2*n.VPA},
"mean.weight.at.age.sp" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.VPA)],ncol=n.VPA,nrow=1,dimnames=list(c("include"),species.names),byrow=TRUE); n<-n+1*n.VPA},
"community.mean.weight.sp" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.VPA)],ncol=n.VPA,nrow=1,dimnames=list(c("include"),species.names),byrow=TRUE); n<-n+1*n.VPA},
"mean.weight.C.sp" ={slot(control,x)<-matrix(opt[n:(n-1+1*n.VPA)],ncol=n.VPA,nrow=1,dimnames=list(c("include"),species.names),byrow=TRUE); n<-n+1*n.VPA},
"community.mean.weight.C.sp" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.VPA)],ncol=n.VPA,nrow=1,dimnames=list(c("include"),species.names),byrow=TRUE); n<-n+1*n.VPA},
"community.F.sp" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.VPA)],ncol=n.VPA,nrow=1,dimnames=list(c("include"),species.names),byrow=TRUE); n<-n+1*n.VPA},
"community.M.sp" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.VPA)],ncol=n.VPA,nrow=1,dimnames=list(c("include"),species.names),byrow=TRUE); n<-n+1*n.VPA},
"life.expectancy.first.age" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.VPA)],ncol=n.VPA,nrow=1,dimnames=list(c("first.age"),species.names),byrow=TRUE); n<-n+1*n.VPA},
"community.life.expectancy.options" = {slot(control,x)<-matrix(opt[n:(n-1+2*n.VPA)],ncol=n.VPA,nrow=2,dimnames=list(c("first.age","weighting"),species.names),byrow=TRUE); n<-n+2*n.VPA},
"size.spectra.sp" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.sp)],ncol=n.sp,nrow=1,dimnames=list(c("include"),all.species.names),byrow=TRUE); n<-n+1*n.sp},
"LFI.sp" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.sp)],ncol=n.sp,nrow=1,dimnames=list(c("include"),all.species.names),byrow=TRUE); n<-n+1*n.sp},
"LFI.age" = {slot(control,x)<-matrix(opt[n:(n-1+1*n.sp)],ncol=n.sp,nrow=1,dimnames=list(c("first.age"),all.species.names),byrow=TRUE); n<-n+1*n.sp},
"community.biomass.small.ages" = {slot(control,x)<-matrix(opt[n:(n-1+2*n.sp)],ncol=n.sp,nrow=2,dimnames=list(c("first.age","last.age"),all.species.names),byrow=TRUE); n<-n+2*n.sp},
"community.biomass.pelagic.ages" = {slot(control,x)<-matrix(opt[n:(n-1+2*n.sp)],ncol=n.sp,nrow=2,dimnames=list(c("first.age","last.age"),all.species.names),byrow=TRUE); n<-n+2*n.sp},
"community.biomass.forage.ages" = {slot(control,x)<-matrix(opt[n:(n-1+2*n.sp)],ncol=n.sp,nrow=2,dimnames=list(c("first.age","last.age"),all.species.names),byrow=TRUE); n<-n+2*n.sp},
# otherwise
{slot(control,x)<-opt[n];n<-n+1}
)
#print(x)
}
control
}
###
## show (a replacement for print of S3 classes)
setMethod("show", signature(object="FLOP.MSFD.control"),
function(object){
n.<-slotNames(object)
for (i in 1:length(n.)) {
cat(n.[i])
for (j in nchar(n.[i]):25) cat(" ")
if (is.integer(slot(object,n.[i]))) cat(slot(object,n.[i]),"\n")
else if (is.vector(slot(object,n.[i]))) {
if (is.list(slot(object,n.[i]))) {
for (k in 1:length(slot(object,n.[i]))) cat("\n\t",slot(object,n.[i])[[k]])
cat("\n")
}
else cat(slot(object,n.[i]),"\n")
}
else if (is.matrix(slot(object,n.[i]))) {
m<-slot(object,n.[i])
cat("\n")
print(m)
}
}
}
)
if (F) {
MSFD<-new("FLOP.MSFD.control")
print(MSFD)
MSFD<-FLOP.MSFD.control()
print(MSFD)
write.FLOP.MSFD.control(MSFD)
a<-read.FLOP.MSFD.control(n.VPA=10,n.other.pred=16)
}