###############################################################################
# AUTHOR(DATE): Agurtzane Urtizberea, Dorleta Garcia
# RESEARCH INSTITUTE: AZTI-TECNALIA
# TITLE: Check variables in a biols object
# NOTE #1: Return plots
###############################################################################
#.......................................................
#....................FUNCTIONS..........................
plot.biols <- function(biols,pdfnm){
require(ggplot2)
require(plyr)
require(FLCore)
names.biols <- names(biols)
path.pdf <- ''
for(i in 1:length(names.biols)){
pdf(paste(path.pdf,names.biols[i],'-',pdfnm,'.pdf',sep=''))
biol <- biols[[i]]
biol.n.df <- as.data.frame(biol@n)
biol.n.df$variable <- 'n'
biol.n.df$indicator <- names.biols[i]
biol.n.df$age <- factor(biol.n.df$age)
biol.wt.df <- as.data.frame(biol@wt)
biol.wt.df$variable <- 'wt'
biol.wt.df$indicator <- names.biols[i]
biol.wt.df$age <- factor(biol.wt.df$age)
df <- rbind(biol.n.df,biol.wt.df)
df$stock <- names.biols[i]
temp <- aggregate(data ~ age+year+stock+indicator+variable, data = df,
mean, na.rm=TRUE,na.action="na.pass")
p <- ggplot(data=temp, aes(x=year, y=data, fill=age)) + geom_line() +
geom_point(size=2, shape=21)+
facet_grid(variable~indicator,scales=c("free_y"))
print(p)
df <- NULL
biol.m.df <- as.data.frame(biol@m)
biol.m.df$variable <- 'm'
biol.m.df$indicator <- names.biols[i]
biol.m.df$age <- factor(biol.n.df$age)
biol.fec.df <- as.data.frame(biol@fec)
biol.fec.df$variable <- 'fec'
biol.fec.df$indicator <- names.biols[i]
biol.fec.df$age <- factor(biol.fec.df$age)
biol.spwn.df <- as.data.frame(biol@spwn)
biol.spwn.df$variable <- 'spwn'
biol.spwn.df$indicator <- names.biols[i]
biol.spwn.df$age <- factor(biol.spwn.df$age)
df <- rbind(biol.m.df,biol.fec.df,biol.spwn.df)
df$stock <- names.biols[i]
temp <- aggregate(data ~ age + year+variable+stock+indicator, data = df,
mean, na.rm=TRUE,na.action="na.pass")
p <- ggplot(data=temp, aes(x=year, y=data, fill=age)) + geom_line() +
geom_point(size=2, shape=21)+
facet_grid(variable~indicator,scales=c("free_y"))
print(p)
df<- NULL
biol.ssb.df <- as.data.frame(ssb(biol))
biol.ssb.df$variable <- 'ssb'
biol.ssb.df$indicator <- names.biols[i]
biol.ssb.df$age <- factor(biol.ssb.df$age)
biol.rec.df <- as.data.frame(rec(biol))
biol.rec.df$variable <- 'rec'
biol.rec.df$indicator <- names.biols[i]
biol.rec.df$age <- factor(biol.rec.df$age)
df <- rbind(biol.ssb.df,biol.rec.df)
df$stock <- names.biols[i]
temp <- aggregate(data ~ age + year+variable+stock+indicator, data = df,
mean, na.rm=TRUE,na.action="na.pass")
p <- ggplot(data=temp, aes(x=year, y=data, fill=age)) + geom_line() +
geom_point(size=2, shape=21)+
facet_grid(variable~indicator,scales=c("free_y"))
print(p)
dev.off()
}
}
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