R/kobe-phaseMar.R
In laurieKell/kobe: Tools for Scientific Fisheries Management Advice
Defines functions
kobePhaseMar
Documented in
kobePhaseMar
utils::globalVariables(c("stock","..count..","group","harvest","run","is","fref"))
#' @importFrom grid grid.newpage pushViewport viewport grid.layout unit
#'
#' @name kobePhaseMar
#' @title Kobe Phase Plot with Marginal Densities
#' @description
#' Plots a Kobe Phase Plot with marginal densities
#' '
#' @aliases kobePhaseMar kobePhaseMar2 kobePhaseMar3
#'
#' @param pts data.frame with stock and harvest variables respresenting points for a year
#' @param trks data.frame with stock and harvest variables respresenting tracks, NULL by default
#' @param mns logical, do you want mean by year of pts be plotted, FALSE by default
#' @param size of points1 by default
#' @param xlab character or expression for x axis title, expression(B:B[MSY]) by default
#' @param ylab character or expression for x axis title, expression(F:F[MSY]) by default
#' @param xlim upper limit of x axis, 2 by default
#' @param ylim upper limit of x axis, 2 by default
#' @param quadcol colours for the quadrants
#' @param col colorRampPalette(c("orange","blue"),space="Lab") by default
#' @param shade .5 by default
#' @param col2 grey(shade) by default
#' @param col3 grey(shade*1.1) by default
#' @param layer a ggplot2 layer to add to phase plot
#' @param bref vertical seperation between quadants and reference line for marginal densities
#' @param fref horizontal seperation between quadants and reference line for marginal densities
#'
#' @return a list with 3 ggplot objects, the 2 marginal densities and the phase plot
#' @export kobePhaseMar
#' @docType methods
#' @rdname kobePhaseMar-method
#'
#' @examples
#' \dontrun{rnorm(10)}
kobePhaseMar=function(pts,trks=NULL,mns=FALSE,size=1,
xlab=expression(B:B[MSY]),
ylab=expression(F:F[MSY]),
xlim=2,ylim=xlim,
quadcol=c("red","green","yellow","yellow"),
col =colorRampPalette(c("orange","blue"),space="Lab"),
shade=.5,col2=grey(shade),col3=grey(shade*1.1),
layer=NULL,
bref=1,fref=1){
if (!("run" %in% names(pts)))
pts=cbind(pts,run=factor(1))
if (!is.null(trks) & !("run" %in% names(trks)))
trks=cbind(trks,run=factor(1))
if ("function" %in% is(col))
col=col(length(unique(pts$run)))
if (length(size)==1) size=rep(size,2)
##### Density plots #############################################################################################
# stock density plot
dS<-ggplot(pts) +
geom_density(aes(x = stock, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
geom_density(aes(x = stock, y = -..count.., fill =run, alpha=0.4)) +
geom_vline(xintercept=bref,col="red",data=data.frame(bref=bref))+
coord_cartesian(xlim=c(0,xlim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.y = element_text(colour='NA'),
axis.text.y = element_text(colour="NA", angle=90),
axis.ticks.y = element_line(colour="NA"),
axis.ticks = element_line(colour="NA"),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0, 0, 0, 1), "lines"),
panel.background = element_rect(fill ="NA", colour="NA"),
panel.border = element_rect(fill ="NA", colour="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA") )
# second density plot, oriented vertically (hence the 'coord_flip()' at the end
dH<-ggplot(pts) +
geom_density(aes(x = harvest, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
geom_density(aes(x = harvest, y = -..count.., fill=run, alpha=0.4)) +
geom_vline(xintercept=fref,col="red",data=data.frame(fref=fref))+
coord_cartesian(xlim=c(0,ylim)) +
#scale_x_continuous(limits=c(0,ylim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.x = element_text(colour ='NA'),
axis.text.x = element_text(colour ="NA"),
axis.ticks.x = element_line(colour ="NA"),
axis.ticks = element_line(colour ="NA"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
plot.margin = unit(c(0, 0, 1, 0), "lines"),
panel.background = element_rect(fill ="NA", colour ="NA"),
panel.border = element_rect(fill ="NA", colour ="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA")
)
# kobe phase plot
kC=kobePhase(pts,quadcol=quadcol,bref=bref) +
geom_point(aes(stock,harvest,group=run),col="black",size=size[1]) +
geom_point(aes(stock,harvest,col=run,group=run),size=size[1]*.5) +
coord_cartesian(xlim=c(0,xlim),ylim=c(0,ylim)) +
scale_colour_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.text.y=element_text(colour="black", angle=90),
plot.margin = unit(c(0, 0, 1, 1), "lines")
)
if ("LayerInstance"%in%is(layer))
kC=kC+layer
else if ("list"%in%is(layer))
if (length(layer)==2)
kC=kC+layer[[1]]+layer[[2]]
if (length(layer)==3)
kC=kC+layer[[1]]+layer[[2]]
# if (length(run)>1){
# dS=dS+scale_fill_manual(values=col)
# dH=dH+scale_fill_manual(values=col)
# kC=kC+scale_colour_manual(values=col)
# }
#
if (mns)
kC=kC+geom_point(aes(stock,harvest,col=run,group=run),size=6.0*size[1], colour="black", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest)))) +
geom_point(aes(stock,harvest,col=run,group=run),size=4.5*size[1], colour="cyan", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest))))
if (!is.null(trks))
kC=kC+geom_path(aes(stock,harvest, col=run,group=run),size=1*size[2], data=trks)
fnVP=function(dH,dS,kC){
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(5, 5))) # 5 by 5 grid
print(dS, vp=vplayout(1,1:4)) # the first density plot will occupy the top of the grid
print(dH +coord_flip(xlim=c(0,ylim)), vp=vplayout(2:5,5)) # 2nd to the left +opts(legend.position = c(0,1.05)) + opts(legend.text = theme_text(colour = "black"))
print(kC, vp=vplayout(2:5,1:4)) # the main x/y plot will instead spread across most of the grid
}
fnVP(dH,dS,kC)
invisible(list(harvest=dH,stock=dS,phase=kC))}
kobePhaseMar2=function(pts,trks=NULL,mns=FALSE,size=1,
xlab=expression(B:B[MSY]),
ylab=expression(F:F[MSY]),
xlim=2,ylim=xlim,
quadcol=c("red","green","yellow","yellow"),
col =colorRampPalette(c("orange","blue"),space="Lab"),
shade=.5,col2=grey(shade),col3=grey(shade*1.1),
layer=NULL,
bref=1,
fref=1,fourth=NULL){
if (!("run" %in% names(pts)))
pts=cbind(pts,run=factor(1))
if (!is.null(trks) & !("run" %in% names(trks)))
trks=cbind(trks,run=factor(1))
if ("function" %in% is(col))
col=col(length(unique(pts$run)))
if (length(size)==1) size=rep(size,2)
##### Density plots #############################################################################################
# stock density plot
dS<-ggplot(pts) +
#geom_density(aes(x = stock, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
geom_density(aes(x = stock, y = ..count.., fill =run, alpha=0.4)) +
geom_vline(xintercept=bref,col="red",data=data.frame(bref=bref))+
coord_cartesian(xlim=c(0,xlim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.y = element_text(colour='NA'),
axis.text.y = element_text(colour="NA", angle=90),
axis.ticks.y = element_line(colour="NA"),
axis.ticks = element_line(colour="NA"),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0, 0, 0, 1), "lines"),
panel.background = element_rect(fill ="NA", colour="NA"),
panel.border = element_rect(fill ="NA", colour="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA") )
# second density plot, oriented vertically (hence the 'coord_flip()' at the end
dH<-ggplot(pts) +
#geom_density(aes(x = harvest, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
geom_density(aes(x = harvest, y = ..count.., fill=run, alpha=0.4)) +
geom_vline(xintercept=fref,col="red",data=data.frame(fref=fref))+
coord_cartesian(xlim=c(0,ylim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.x = element_text(colour ='NA'),
axis.text.x = element_text(colour ="NA"),
axis.ticks.x = element_line(colour ="NA"),
axis.ticks = element_line(colour ="NA"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
plot.margin = unit(c(0, 0, 1, 0), "lines"),
panel.background = element_rect(fill ="NA", colour ="NA"),
panel.border = element_rect(fill ="NA", colour ="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA")
)
# kobe phase plot
kC=kobePhase(pts,quadcol=quadcol,bref=bref,fref=fref) +
geom_point(aes(stock,harvest,group=run),col="black",size=size[1]) +
geom_point(aes(stock,harvest,col=run,group=run),size=size[1]*.5) +
coord_cartesian(xlim=c(0,xlim),ylim=c(0,ylim)) +
scale_colour_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.text.y = element_text(colour="black", angle=90),
plot.margin = unit(c(0, 0, 1, 1), "lines"))
if ("LayerInstance"%in%is(layer))
kC=kC+layer
else if ("list"%in%is(layer))
kC=kC+layer[[1]]+layer[[2]]
# if (length(run)>1){
# dS=dS+scale_fill_manual(values=col)
# dH=dH+scale_fill_manual(values=col)
# kC=kC+scale_colour_manual(values=col)
# }
#
if (mns)
kC=kC+geom_point(aes(stock,harvest,col=run,group=run),size=6.0*size[1], colour="black", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest)))) +
geom_point(aes(stock,harvest,col=run,group=run),size=4.5*size[1], colour="cyan", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest))))
if (!is.null(trks))
kC=kC+geom_path(aes(stock,harvest, col=run,group=run),size=1*size[2], data=trks)
fnVP=function(dH,dS,kC,fourth=fourth){
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(5, 5))) # 5 by 5 grid
print(dS, vp=vplayout(1,1:4)) # the first density plot will occupy the top of the grid
print(dH +coord_flip(xlim=c(0,ylim)), vp=vplayout(2:5,5)) # 2nd to the left +opts(legend.position = c(0,1.05)) + opts(legend.text = theme_text(colour = "black"))
print(kC, vp=vplayout(2:5,1:4)) # the main x/y plot will instead spread across most of the grid
if (!is.null(fourth)) print(fourth, vp=vplayout(1,5))
}
if (!is.null(fourth))
fourth=fourth+
theme(legend.position = "none",
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.ticks = element_blank(),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0, 0, 0, 0), "lines"),
panel.background = element_rect(fill ="NA", colour="NA"),
panel.border = element_rect(fill ="NA", colour="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA") )
fnVP(dH,dS,kC,fourth)
invisible(list(harvest=dH,stock=dS,phase=kC))}
kobePhaseMar3=function(pts,trks=NULL,mns=FALSE,size=1,
xlab=expression(B:B[MSY]),
ylab=expression(F:F[MSY]),
xlim=2,ylim=xlim,
quadcol=c("red","green","yellow","yellow"),
col =colorRampPalette(c("orange","blue"),space="Lab"),
shade=.5,col2=grey(shade),col3=grey(shade*1.1),
layer=NULL,
bref=1,fref=1){
if (!("run" %in% names(pts)))
pts=cbind(pts,run=factor(1))
if (!is.null(trks) & !("run" %in% names(trks)))
trks=cbind(trks,run=factor(1))
if ("function" %in% is(col))
col=col(length(unique(pts$run)))
if (length(size)==1) size=rep(size,2)
##### Density plots #############################################################################################
# stock density plot
dS<-ggplot(pts) +
geom_density(aes(x = stock, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
#geom_density(aes(x = stock, y = ..count.., fill =run, alpha=0.4)) +
geom_vline(xintercept=bref,col="red",data=data.frame(bref=bref))+
coord_cartesian(xlim=c(0,xlim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.y = element_text(colour='NA'),
axis.text.y = element_text(colour="NA", angle=90),
axis.ticks.y = element_line(colour="NA"),
axis.ticks = element_line(colour="NA"),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0, 0, 0, 1), "lines"),
panel.background = element_rect(fill ="NA", colour="NA"),
panel.border = element_rect(fill ="NA", colour="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA") )
# second density plot, oriented vertically (hence the 'coord_flip()' at the end
dH<-ggplot(pts) +
geom_density(aes(x = harvest, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
#geom_density(aes(x = harvest, y = ..count.., fill=run, alpha=0.4)) +
geom_vline(xintercept=fref,col="red",data=data.frame(fref=fref))+
coord_cartesian(ylim=c(0,ylim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.x = element_text(colour ='NA'),
axis.text.x = element_text(colour ="NA"),
axis.ticks.x = element_line(colour ="NA"),
axis.ticks = element_line(colour ="NA"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
plot.margin = unit(c(0, 0, 1, 0), "lines"),
panel.background = element_rect(fill ="NA", colour ="NA"),
panel.border = element_rect(fill ="NA", colour ="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA")
)
# kobe phase plot
kC=kobePhase(pts,quadcol=quadcol,bref=bref,fref=fref) +
geom_point(aes(stock,harvest,group=run),col="black",size=size[1]) +
geom_point(aes(stock,harvest,col=run,group=run),size=size[1]*.5) +
coord_cartesian(xlim=c(0,xlim),ylim=c(0,ylim)) +
scale_colour_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.text.y = element_text(colour="black", angle=90),
plot.margin = unit(c(0, 0, 1, 1), "lines"))
if ("LayerInstance"%in%is(layer))
kC=kC+layer
else if ("list"%in%is(layer))
kC=kC+layer[[1]]+layer[[2]]
# if (length(run)>1){
# dS=dS+scale_fill_manual(values=col)
# dH=dH+scale_fill_manual(values=col)
# kC=kC+scale_colour_manual(values=col)
# }
#
if (mns)
kC=kC+geom_point(aes(stock,harvest,col=run,group=run),size=6.0*size[1], colour="black", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest)))) +
geom_point(aes(stock,harvest,col=run,group=run),size=4.5*size[1], colour="cyan", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest))))
if (!is.null(trks))
kC=kC+geom_path(aes(stock,harvest,col=run,group=run),size=1*size[2], data=trks)
fnVP=function(dH,dS,kC){
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(5, 5))) # 5 by 5 grid
print(dS, vp=vplayout(1,1:4)) # the first density plot will occupy the top of the grid
print(dH +coord_flip(xlim=c(0,ylim)), vp=vplayout(2:5,5)) # 2nd to the left +opts(legend.position = c(0,1.05)) + opts(legend.text = theme_text(colour = "black"))
print(kC, vp=vplayout(2:5,1:4)) # the main x/y plot will instead spread across most of the grid
}
fnVP(dH,dS,kC)
invisible(list(harvest=dH,stock=dS,phase=kC))}
laurieKell/kobe documentation built on Sept. 9, 2023, 9:47 p.m.
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Defines functions kobePhaseMar
Documented in kobePhaseMar
utils::globalVariables(c("stock","..count..","group","harvest","run","is","fref"))
#' @importFrom grid grid.newpage pushViewport viewport grid.layout unit
#'
#' @name kobePhaseMar
#' @title Kobe Phase Plot with Marginal Densities
#' @description
#' Plots a Kobe Phase Plot with marginal densities
#' '
#' @aliases kobePhaseMar kobePhaseMar2 kobePhaseMar3
#'
#' @param pts data.frame with stock and harvest variables respresenting points for a year
#' @param trks data.frame with stock and harvest variables respresenting tracks, NULL by default
#' @param mns logical, do you want mean by year of pts be plotted, FALSE by default
#' @param size of points1 by default
#' @param xlab character or expression for x axis title, expression(B:B[MSY]) by default
#' @param ylab character or expression for x axis title, expression(F:F[MSY]) by default
#' @param xlim upper limit of x axis, 2 by default
#' @param ylim upper limit of x axis, 2 by default
#' @param quadcol colours for the quadrants
#' @param col colorRampPalette(c("orange","blue"),space="Lab") by default
#' @param shade .5 by default
#' @param col2 grey(shade) by default
#' @param col3 grey(shade*1.1) by default
#' @param layer a ggplot2 layer to add to phase plot
#' @param bref vertical seperation between quadants and reference line for marginal densities
#' @param fref horizontal seperation between quadants and reference line for marginal densities
#'
#' @return a list with 3 ggplot objects, the 2 marginal densities and the phase plot
#' @export kobePhaseMar
#' @docType methods
#' @rdname kobePhaseMar-method
#'
#' @examples
#' \dontrun{rnorm(10)}
kobePhaseMar=function(pts,trks=NULL,mns=FALSE,size=1,
xlab=expression(B:B[MSY]),
ylab=expression(F:F[MSY]),
xlim=2,ylim=xlim,
quadcol=c("red","green","yellow","yellow"),
col =colorRampPalette(c("orange","blue"),space="Lab"),
shade=.5,col2=grey(shade),col3=grey(shade*1.1),
layer=NULL,
bref=1,fref=1){
if (!("run" %in% names(pts)))
pts=cbind(pts,run=factor(1))
if (!is.null(trks) & !("run" %in% names(trks)))
trks=cbind(trks,run=factor(1))
if ("function" %in% is(col))
col=col(length(unique(pts$run)))
if (length(size)==1) size=rep(size,2)
##### Density plots #############################################################################################
# stock density plot
dS<-ggplot(pts) +
geom_density(aes(x = stock, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
geom_density(aes(x = stock, y = -..count.., fill =run, alpha=0.4)) +
geom_vline(xintercept=bref,col="red",data=data.frame(bref=bref))+
coord_cartesian(xlim=c(0,xlim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.y = element_text(colour='NA'),
axis.text.y = element_text(colour="NA", angle=90),
axis.ticks.y = element_line(colour="NA"),
axis.ticks = element_line(colour="NA"),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0, 0, 0, 1), "lines"),
panel.background = element_rect(fill ="NA", colour="NA"),
panel.border = element_rect(fill ="NA", colour="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA") )
# second density plot, oriented vertically (hence the 'coord_flip()' at the end
dH<-ggplot(pts) +
geom_density(aes(x = harvest, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
geom_density(aes(x = harvest, y = -..count.., fill=run, alpha=0.4)) +
geom_vline(xintercept=fref,col="red",data=data.frame(fref=fref))+
coord_cartesian(xlim=c(0,ylim)) +
#scale_x_continuous(limits=c(0,ylim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.x = element_text(colour ='NA'),
axis.text.x = element_text(colour ="NA"),
axis.ticks.x = element_line(colour ="NA"),
axis.ticks = element_line(colour ="NA"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
plot.margin = unit(c(0, 0, 1, 0), "lines"),
panel.background = element_rect(fill ="NA", colour ="NA"),
panel.border = element_rect(fill ="NA", colour ="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA")
)
# kobe phase plot
kC=kobePhase(pts,quadcol=quadcol,bref=bref) +
geom_point(aes(stock,harvest,group=run),col="black",size=size[1]) +
geom_point(aes(stock,harvest,col=run,group=run),size=size[1]*.5) +
coord_cartesian(xlim=c(0,xlim),ylim=c(0,ylim)) +
scale_colour_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.text.y=element_text(colour="black", angle=90),
plot.margin = unit(c(0, 0, 1, 1), "lines")
)
if ("LayerInstance"%in%is(layer))
kC=kC+layer
else if ("list"%in%is(layer))
if (length(layer)==2)
kC=kC+layer[[1]]+layer[[2]]
if (length(layer)==3)
kC=kC+layer[[1]]+layer[[2]]
# if (length(run)>1){
# dS=dS+scale_fill_manual(values=col)
# dH=dH+scale_fill_manual(values=col)
# kC=kC+scale_colour_manual(values=col)
# }
#
if (mns)
kC=kC+geom_point(aes(stock,harvest,col=run,group=run),size=6.0*size[1], colour="black", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest)))) +
geom_point(aes(stock,harvest,col=run,group=run),size=4.5*size[1], colour="cyan", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest))))
if (!is.null(trks))
kC=kC+geom_path(aes(stock,harvest, col=run,group=run),size=1*size[2], data=trks)
fnVP=function(dH,dS,kC){
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(5, 5))) # 5 by 5 grid
print(dS, vp=vplayout(1,1:4)) # the first density plot will occupy the top of the grid
print(dH +coord_flip(xlim=c(0,ylim)), vp=vplayout(2:5,5)) # 2nd to the left +opts(legend.position = c(0,1.05)) + opts(legend.text = theme_text(colour = "black"))
print(kC, vp=vplayout(2:5,1:4)) # the main x/y plot will instead spread across most of the grid
}
fnVP(dH,dS,kC)
invisible(list(harvest=dH,stock=dS,phase=kC))}
kobePhaseMar2=function(pts,trks=NULL,mns=FALSE,size=1,
xlab=expression(B:B[MSY]),
ylab=expression(F:F[MSY]),
xlim=2,ylim=xlim,
quadcol=c("red","green","yellow","yellow"),
col =colorRampPalette(c("orange","blue"),space="Lab"),
shade=.5,col2=grey(shade),col3=grey(shade*1.1),
layer=NULL,
bref=1,
fref=1,fourth=NULL){
if (!("run" %in% names(pts)))
pts=cbind(pts,run=factor(1))
if (!is.null(trks) & !("run" %in% names(trks)))
trks=cbind(trks,run=factor(1))
if ("function" %in% is(col))
col=col(length(unique(pts$run)))
if (length(size)==1) size=rep(size,2)
##### Density plots #############################################################################################
# stock density plot
dS<-ggplot(pts) +
#geom_density(aes(x = stock, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
geom_density(aes(x = stock, y = ..count.., fill =run, alpha=0.4)) +
geom_vline(xintercept=bref,col="red",data=data.frame(bref=bref))+
coord_cartesian(xlim=c(0,xlim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.y = element_text(colour='NA'),
axis.text.y = element_text(colour="NA", angle=90),
axis.ticks.y = element_line(colour="NA"),
axis.ticks = element_line(colour="NA"),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0, 0, 0, 1), "lines"),
panel.background = element_rect(fill ="NA", colour="NA"),
panel.border = element_rect(fill ="NA", colour="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA") )
# second density plot, oriented vertically (hence the 'coord_flip()' at the end
dH<-ggplot(pts) +
#geom_density(aes(x = harvest, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
geom_density(aes(x = harvest, y = ..count.., fill=run, alpha=0.4)) +
geom_vline(xintercept=fref,col="red",data=data.frame(fref=fref))+
coord_cartesian(xlim=c(0,ylim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.x = element_text(colour ='NA'),
axis.text.x = element_text(colour ="NA"),
axis.ticks.x = element_line(colour ="NA"),
axis.ticks = element_line(colour ="NA"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
plot.margin = unit(c(0, 0, 1, 0), "lines"),
panel.background = element_rect(fill ="NA", colour ="NA"),
panel.border = element_rect(fill ="NA", colour ="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA")
)
# kobe phase plot
kC=kobePhase(pts,quadcol=quadcol,bref=bref,fref=fref) +
geom_point(aes(stock,harvest,group=run),col="black",size=size[1]) +
geom_point(aes(stock,harvest,col=run,group=run),size=size[1]*.5) +
coord_cartesian(xlim=c(0,xlim),ylim=c(0,ylim)) +
scale_colour_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.text.y = element_text(colour="black", angle=90),
plot.margin = unit(c(0, 0, 1, 1), "lines"))
if ("LayerInstance"%in%is(layer))
kC=kC+layer
else if ("list"%in%is(layer))
kC=kC+layer[[1]]+layer[[2]]
# if (length(run)>1){
# dS=dS+scale_fill_manual(values=col)
# dH=dH+scale_fill_manual(values=col)
# kC=kC+scale_colour_manual(values=col)
# }
#
if (mns)
kC=kC+geom_point(aes(stock,harvest,col=run,group=run),size=6.0*size[1], colour="black", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest)))) +
geom_point(aes(stock,harvest,col=run,group=run),size=4.5*size[1], colour="cyan", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest))))
if (!is.null(trks))
kC=kC+geom_path(aes(stock,harvest, col=run,group=run),size=1*size[2], data=trks)
fnVP=function(dH,dS,kC,fourth=fourth){
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(5, 5))) # 5 by 5 grid
print(dS, vp=vplayout(1,1:4)) # the first density plot will occupy the top of the grid
print(dH +coord_flip(xlim=c(0,ylim)), vp=vplayout(2:5,5)) # 2nd to the left +opts(legend.position = c(0,1.05)) + opts(legend.text = theme_text(colour = "black"))
print(kC, vp=vplayout(2:5,1:4)) # the main x/y plot will instead spread across most of the grid
if (!is.null(fourth)) print(fourth, vp=vplayout(1,5))
}
if (!is.null(fourth))
fourth=fourth+
theme(legend.position = "none",
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.ticks = element_blank(),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0, 0, 0, 0), "lines"),
panel.background = element_rect(fill ="NA", colour="NA"),
panel.border = element_rect(fill ="NA", colour="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA") )
fnVP(dH,dS,kC,fourth)
invisible(list(harvest=dH,stock=dS,phase=kC))}
kobePhaseMar3=function(pts,trks=NULL,mns=FALSE,size=1,
xlab=expression(B:B[MSY]),
ylab=expression(F:F[MSY]),
xlim=2,ylim=xlim,
quadcol=c("red","green","yellow","yellow"),
col =colorRampPalette(c("orange","blue"),space="Lab"),
shade=.5,col2=grey(shade),col3=grey(shade*1.1),
layer=NULL,
bref=1,fref=1){
if (!("run" %in% names(pts)))
pts=cbind(pts,run=factor(1))
if (!is.null(trks) & !("run" %in% names(trks)))
trks=cbind(trks,run=factor(1))
if ("function" %in% is(col))
col=col(length(unique(pts$run)))
if (length(size)==1) size=rep(size,2)
##### Density plots #############################################################################################
# stock density plot
dS<-ggplot(pts) +
geom_density(aes(x = stock, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
#geom_density(aes(x = stock, y = ..count.., fill =run, alpha=0.4)) +
geom_vline(xintercept=bref,col="red",data=data.frame(bref=bref))+
coord_cartesian(xlim=c(0,xlim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.y = element_text(colour='NA'),
axis.text.y = element_text(colour="NA", angle=90),
axis.ticks.y = element_line(colour="NA"),
axis.ticks = element_line(colour="NA"),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
plot.margin = unit(c(0, 0, 0, 1), "lines"),
panel.background = element_rect(fill ="NA", colour="NA"),
panel.border = element_rect(fill ="NA", colour="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA") )
# second density plot, oriented vertically (hence the 'coord_flip()' at the end
dH<-ggplot(pts) +
geom_density(aes(x = harvest, y = ..count.., group=run), fill=col2, col=col3, position = "stack") +
#geom_density(aes(x = harvest, y = ..count.., fill=run, alpha=0.4)) +
geom_vline(xintercept=fref,col="red",data=data.frame(fref=fref))+
coord_cartesian(ylim=c(0,ylim)) +
scale_fill_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.title.x = element_text(colour ='NA'),
axis.text.x = element_text(colour ="NA"),
axis.ticks.x = element_line(colour ="NA"),
axis.ticks = element_line(colour ="NA"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
plot.margin = unit(c(0, 0, 1, 0), "lines"),
panel.background = element_rect(fill ="NA", colour ="NA"),
panel.border = element_rect(fill ="NA", colour ="NA"),
panel.grid.major = element_line(colour ="NA"),
panel.grid.minor = element_line(colour ="NA")
)
# kobe phase plot
kC=kobePhase(pts,quadcol=quadcol,bref=bref,fref=fref) +
geom_point(aes(stock,harvest,group=run),col="black",size=size[1]) +
geom_point(aes(stock,harvest,col=run,group=run),size=size[1]*.5) +
coord_cartesian(xlim=c(0,xlim),ylim=c(0,ylim)) +
scale_colour_manual(values=col) +
xlab(xlab) + ylab(ylab) +
theme(legend.position = "none",
axis.text.y = element_text(colour="black", angle=90),
plot.margin = unit(c(0, 0, 1, 1), "lines"))
if ("LayerInstance"%in%is(layer))
kC=kC+layer
else if ("list"%in%is(layer))
kC=kC+layer[[1]]+layer[[2]]
# if (length(run)>1){
# dS=dS+scale_fill_manual(values=col)
# dH=dH+scale_fill_manual(values=col)
# kC=kC+scale_colour_manual(values=col)
# }
#
if (mns)
kC=kC+geom_point(aes(stock,harvest,col=run,group=run),size=6.0*size[1], colour="black", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest)))) +
geom_point(aes(stock,harvest,col=run,group=run),size=4.5*size[1], colour="cyan", data=ddply(pts,.(run),function(x) data.frame(stock=median(x$stock),harvest=median(x$harvest))))
if (!is.null(trks))
kC=kC+geom_path(aes(stock,harvest,col=run,group=run),size=1*size[2], data=trks)
fnVP=function(dH,dS,kC){
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(5, 5))) # 5 by 5 grid
print(dS, vp=vplayout(1,1:4)) # the first density plot will occupy the top of the grid
print(dH +coord_flip(xlim=c(0,ylim)), vp=vplayout(2:5,5)) # 2nd to the left +opts(legend.position = c(0,1.05)) + opts(legend.text = theme_text(colour = "black"))
print(kC, vp=vplayout(2:5,1:4)) # the main x/y plot will instead spread across most of the grid
}
fnVP(dH,dS,kC)
invisible(list(harvest=dH,stock=dS,phase=kC))}
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