R/plots_therMizer.R
In pwoodworth-jefcoats/Size-Based-Modeling: Mizer With The Effects Of Temperature Included
# Plotting methods for the therMizerSim class
# Copyright 2012 Finlay Scott and Julia Blanchard.
# Distributed under the GPL 2 or later
# Maintainer of mizer package: Finlay Scott, CEFAS
# Modified for therMizer by: Phoebe.Woodworth-Jefcoats@noaa.gov
# Added ability to plot temperature effects
# Changed summary plot figure to include these figures
# Hackiness to get past the 'no visible binding ... ' warning when running check
utils::globalVariables(c("time", "value", "Species", "w", "gear"))
# Biomass through time
# Pretty easy - user could do it themselves by hand for fine tuning if necessary
#' Plot the biomass of each species through time
#'
#' After running a projection, the biomass of each species can be plotted
#' against time. The biomass is calculated within user defined size limits (see
#' \code{\link{getBiomass}}). This plot is pretty easy to do by hand. It just
#' gets the biomass using the \code{\link{getBiomass}} method and plots using
#' the ggplot2 package. You can then fiddle about with colours and linetypes
#' etc. Just look at the source code for details.
#'
#' @param object An object of class \code{therMizerSim}.
#' @param start_time The first time step to be plotted. Default is the beginning
#' of the time series.
#' @param end_time The first time step to be plotted. Default is the end of the
#' time series.
#' @param print_it Display the plot, or just return the ggplot2 object. Default
#' value is TRUE
#' @param ... Other arguments to pass to \code{getBiomass} method, for example
#' \code{min_w} and \code{max_w}
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getBiomass}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotBiomass(sim)
#' plotBiomass(sim, min_w = 10, max_w = 1000)
#' }
setGeneric('plotBiomass', function(object, ...)
standardGeneric('plotBiomass'))
#' Plot the biomass using a \code{therMizerSim} object.
#' @rdname plotBiomass
setMethod('plotBiomass', signature(object='therMizerSim'),
function(object, print_it=TRUE, start_time=as.numeric(dimnames(object@n)[[1]][1]), end_time = as.numeric(dimnames(object@n)[[1]][dim(object@n)[1]]), ...){
b <- getBiomass(object, ...)
names(dimnames(b))[names(dimnames(b))=="sp"] <- "Species"
if(start_time >= end_time){
stop("start_time must be less than end_time")
}
b <- b[(as.numeric(dimnames(b)[[1]]) >= start_time) & (as.numeric(dimnames(b)[[1]]) <= end_time),,drop=FALSE]
bm <- melt(b)
# Force Species column to be a character (if numbers used - may be
# interpreted as integer and hence continuous)
bm$Species <- as.character(bm$Species)
# Due to log10, need to set a minimum value, seems like a feature in ggplot
min_value <- 1e-300
bm <- bm[bm$value >= min_value,]
p <- ggplot(bm) + geom_line(aes(x=time,y=value, colour=Species, linetype=Species)) + scale_y_continuous(trans="log10", name="Biomass") + scale_x_continuous(name="Time")
if (nrow(object@params@species_params)>12){
p <- ggplot(bm) + geom_line(aes(x=time,y=value, group=Species)) + scale_y_continuous(trans="log10", name="Biomass") + scale_x_continuous(name="Time")
}
if (print_it)
print(p)
return(p)
}
)
#' Plot the total yield of each species through time
#'
#' After running a projection, the total yield of each species across all
#' fishing gears can be plotted against time. This plot is pretty easy to do by
#' hand. It just gets the biomass using the \code{\link{getYield}} method and
#' plots using the ggplot2 package. You can then fiddle about with colours and
#' linetypes etc. Just look at the source code for details.
#'
#' @param object An object of class \code{therMizerSim}
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getYield} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getYield}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotYield(sim)
#' }
setGeneric('plotYield', function(object, ...)
standardGeneric('plotYield'))
#' Plot the yield using a \code{therMizerSim} object.
#' @rdname plotYield
setMethod('plotYield', signature(object='therMizerSim'),
function(object, print_it = TRUE, ...){
y <- getYield(object, ...)
names(dimnames(y))[names(dimnames(y))=="sp"] <- "Species"
ym <- melt(y)
p <- ggplot(ym) + geom_line(aes(x=time,y=value, colour=Species, linetype=Species)) + scale_y_continuous(trans="log10", name="Yield") + scale_x_continuous(name="Time")
if (nrow(object@params@species_params)>12){
p <- ggplot(ym) + geom_line(aes(x=time,y=value, group=Species)) + scale_y_continuous(trans="log10", name="Yield") + scale_x_continuous(name="Time")
}
if (print_it)
print(p)
return(p)
}
)
#' Plot the total yield of each species by gear through time
#'
#' After running a projection, the total yield of each species by fishing gear
#' can be plotted against time. This plot is pretty easy to do by hand. It just
#' gets the biomass using the \code{\link{getYieldGear}} method and plots using
#' the ggplot2 package. You can then fiddle about with colours and linetypes
#' etc. Just look at the source code for details.
#'
#' @param object An object of class \code{therMizerSim}
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getYieldGear} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getYieldGear}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotYieldGear(sim)
#' }
setGeneric('plotYieldGear', function(object, ...)
standardGeneric('plotYieldGear'))
#' Plot the yield of each gear using a \code{therMizerSim} object.
#' @rdname plotYieldGear
setMethod('plotYieldGear', signature(object='therMizerSim'),
function(object, print_it=TRUE, ...){
y <- getYieldGear(object, ...)
names(dimnames(y))[names(dimnames(y))=="sp"] <- "Species"
ym <- melt(y)
p <- ggplot(ym) + geom_line(aes(x=time,y=value, colour=Species, linetype=gear)) + scale_y_continuous(trans="log10", name="Yield") + scale_x_continuous(name="Time")
if (nrow(object@params@species_params)>12){
p <- ggplot(ym) + geom_line(aes(x=time,y=value, group=Species)) + scale_y_continuous(trans="log10", name="Yield") + scale_x_continuous(name="Time")
}
if (print_it)
print(p)
return(p)
}
)
#' Plot the abundance spectra of each species and the background population
#'
#' After running a projection, the spectra of the abundance of each species and
#' the background population can be plotted. The abundance is averaged over the
#' specified time range (a single value for the time range can be used to plot a
#' single time step). The abundance can be in terms of numbers or biomass,
#' depending on the \code{biomass} argument.
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param min_w Minimum weight to be plotted (useful for truncating the
#' background spectrum). Default value is a hundredth of the minimum size
#' value of the community.
#' @param biomass A boolean value. Should the biomass spectrum (TRUE) be plotted
#' or the abundance in numbers (FALSE). Default is TRUE.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments (currently unused)
#'
#' @return A ggplot2 object
#' @export
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotSpectra(sim)
#' plotSpectra(sim, min_w = 1e-6)
#' plotSpectra(sim, time_range = 10:20)
#' plotSpectra(sim, time_range = 10:20, biomass = FALSE)
#' }
setGeneric('plotSpectra', function(object, ...)
standardGeneric('plotSpectra'))
#' Plot the abundance spectra using a \code{therMizerSim} object.
#' @rdname plotSpectra
setMethod('plotSpectra', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), min_w =min(object@params@w)/100, biomass = TRUE, print_it = TRUE, ...){
time_elements <- get_time_elements(object,time_range)
spec_n <- apply(object@n[time_elements,,,drop=FALSE],c(2,3), mean)
background_n <- apply(object@n_pp[time_elements,,drop=FALSE],2,mean)
y_axis_name = "Abundance"
if (biomass){
spec_n <- sweep(spec_n,2,object@params@w,"*")
background_n <- background_n * object@params@w_full
y_axis_name = "Biomass"
}
# Make data.frame for plot
plot_dat <- data.frame(value = c(spec_n), Species = dimnames(spec_n)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
plot_dat <- rbind(plot_dat, data.frame(value = c(background_n), Species = "Background", w = object@params@w_full))
# lop off 0s in background and apply min_w
plot_dat <- plot_dat[(plot_dat$value > 0) & (plot_dat$w >= min_w),]
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = y_axis_name, trans="log10")
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = y_axis_name, trans="log10")
}
if (print_it)
print(p)
return(p)
}
)
#' Plot the feeding level of each species by size
#'
#' After running a projection, plot the feeding level of each species by size.
#' The feeding level is averaged over the specified time range (a single value
#' for the time range can be used).
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getFeedingLevel} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getFeedingLevel}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotFeedingLevel(sim)
#' plotFeedingLevel(sim, time_range = 10:20)
#' }
setGeneric('plotFeedingLevel', function(object, ...)
standardGeneric('plotFeedingLevel'))
#' PLot the feeding level using a \code{therMizerSim} object.
#' @rdname plotFeedingLevel
setMethod('plotFeedingLevel', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
feed_time <- getFeedingLevel(object=object, time_range=time_range, drop=FALSE, ...)
feed <- apply(feed_time, c(2,3), mean)
plot_dat <- data.frame(value = c(feed), Species = dimnames(feed)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Feeding Level", limits=c(0,1))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Feeding Level", limits=c(0,1))
}
if (print_it)
print(p)
return(p)
}
)
#' Plot M2 of each species by size
#'
#' After running a projection, plot M2 of each species by size. M2 is averaged
#' over the specified time range (a single value for the time range can be used
#' to plot a single time step).
#'
#' @param object An object of class \code{therMizerSim}
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getM2} method.
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getM2}}
#' @seealso \code{\link{getM2}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotM2(sim)
#' plotM2(sim, time_range = 10:20)
#' }
setGeneric('plotM2', function(object, ...)
standardGeneric('plotM2'))
#' Plot M2 using a \code{therMizerSim} object.
#' @rdname plotM2
setMethod('plotM2', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
m2_time <- getM2(object, time_range=time_range, drop=FALSE, ...)
m2 <- apply(m2_time, c(2,3), mean)
plot_dat <- data.frame(value = c(m2), Species = dimnames(m2)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "M2", limits=c(0,max(plot_dat$value)))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "M2", limits=c(0,max(plot_dat$value)))
}
if (print_it)
print(p)
return(p)
}
)
#' Plot total fishing mortality of each species by size
#'
#' After running a projection, plot the total fishing mortality of each species
#' by size. The total fishing mortality is averaged over the specified time
#' range (a single value for the time range can be used to plot a single time
#' step).
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getFMort} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getFMort}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotFMort(sim)
#' plotFMort(sim, time_range = 10:20)
#' }
setGeneric('plotFMort', function(object, ...)
standardGeneric('plotFMort'))
#' Plot total fishing mortality using a \code{therMizerSim} object.
#' @rdname plotFMort
setMethod('plotFMort', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
f_time <- getFMort(object, time_range=time_range, drop=FALSE, ...)
f <- apply(f_time, c(2,3), mean)
plot_dat <- data.frame(value = c(f), Species = dimnames(f)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Total fishing mortality", limits=c(0,max(plot_dat$value)))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Total fishing mortality", limits=c(0,max(plot_dat$value)))
}
if (print_it)
print(p)
return(p)
}
)
#' Plot total temperature effect on encounter rate on each species by size
#'
#' After running a projection, plot the temperature effect on encounter rate
#' for each species by size. The total temperature effect is averaged over
#' the specified time range (a single value for the time range can be used
#' to plot a single time step).
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getFMort} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getTempEffect}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotTempEffectEncount(sim)
#' plotTempEffectEncount(sim, time_range = 10:20)
#' }
setGeneric('plotTempEffectEncount', function(object, ...)
standardGeneric('plotTempEffectEncount'))
#' Plot total temperature effect using a \code{therMizerSim} object.
#' @rdname plotTempEffectEncount
setMethod('plotTempEffectEncount', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
te_time <- getTempEffectEncount(object, time_range=time_range, drop=FALSE, ...)
te <- apply(te_time, c(2,3), mean)
plot_dat <- data.frame(value = c(te), Species = dimnames(te)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Temperature Effect - Encounter", limits=c(0,max(plot_dat$value)))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Temperature Effect - Encounter", limits=c(0,max(plot_dat$value)))
}
if (print_it)
print(p)
return(p)
}
)
#' Plot total temperature effect on metabolism on each species by size
#'
#' After running a projection, plot the temperature effect on metabolism for
#' each species by size. The total temperature effect is averaged over the
#' specified time range (a single value for the time range can be used to
#' plot a single time step).
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getFMort} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getTempEffect}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotTempEffectMetab(sim)
#' plotTempEffectMetab(sim, time_range = 10:20)
#' }
setGeneric('plotTempEffectMetab', function(object, ...)
standardGeneric('plotTempEffectMetab'))
#' Plot total temperature effect using a \code{therMizerSim} object.
#' @rdname plotTempEffectMetab
setMethod('plotTempEffectMetab', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
te_time <- getTempEffectMetab(object, time_range=time_range, drop=FALSE, ...)
te <- apply(te_time, c(2,3), mean)
plot_dat <- data.frame(value = c(te), Species = dimnames(te)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Temperature Effect - Metabolism", limits=c(0,max(plot_dat$value)))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Temperature Effect - Metabolism", limits=c(0,max(plot_dat$value)))
}
if (print_it)
print(p)
return(p)
}
)
#' Summary plot for \code{therMizerSim} objects
#'
#' After running a projection, produces 6 plots in the same window: feeding
#' level, predation mortality, fishing mortality, and temperature effects on
#' metabolism and encounter rate for each species by size; and biomass of
#' each species through time. This method just uses the other plotting
#' methods and puts them all in one window.
#'
#' @param x An object of class \code{therMizerSim}
#' @param y Not used
#' @param ... For additional arguments see the documentation for
#' \code{\link{plotBiomass}},
#' \code{\link{plotFeedingLevel}},\code{\link{plotM2}},
#' \code{\link{plotTempEffectEncount}},
#' \code{\link{plotTempEffectMetab}},
#' and \code{\link{plotFMort}}.
#' @return A viewport object
#' @export
#' @rdname plot_therMizer
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plot(sim)
#' plot(sim, time_range = 10:20) # change time period for size-based plots
#' plot(sim, min_w = 10, max_w = 1000) # change size range for biomass plot
#' }
setMethod("plot", signature(x="therMizerSim", y="missing"),
function(x, ...){
p1 <- plotFeedingLevel(x,print_it = FALSE,...)
p2 <- plotBiomass(x,print_it = FALSE,...)
p3 <- plotM2(x,print_it = FALSE,...)
p4 <- plotFMort(x,print_it = FALSE,...)
p5 <- plotTempEffectEncount(x,print_it = FALSE,...)
p6 <- plotTempEffectMetab(x,print_it = FALSE,...)
grid.newpage()
glayout <- grid.layout(3,2) # widths and heights arguments
vp <- viewport(layout = glayout)
pushViewport(vp)
vplayout <- function(x,y)
viewport(layout.pos.row=x, layout.pos.col = y)
print(p1+ theme(legend.position="none"), vp = vplayout(1,1))
print(p2+ theme(legend.position="none"), vp = vplayout(1,2))
print(p3+ theme(legend.position="none"), vp = vplayout(2,1))
print(p4+ theme(legend.position="none"), vp = vplayout(2,2))
print(p5+ theme(legend.position="none"), vp = vplayout(3,1))
print(p6+ theme(legend.position="right", legend.key.size=unit(0.4,"cm")), vp = vplayout(3,2))
}
)
pwoodworth-jefcoats/Size-Based-Modeling documentation built on Sept. 15, 2023, 8:13 a.m.
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# Plotting methods for the therMizerSim class
# Copyright 2012 Finlay Scott and Julia Blanchard.
# Distributed under the GPL 2 or later
# Maintainer of mizer package: Finlay Scott, CEFAS
# Modified for therMizer by: Phoebe.Woodworth-Jefcoats@noaa.gov
# Added ability to plot temperature effects
# Changed summary plot figure to include these figures
# Hackiness to get past the 'no visible binding ... ' warning when running check
utils::globalVariables(c("time", "value", "Species", "w", "gear"))
# Biomass through time
# Pretty easy - user could do it themselves by hand for fine tuning if necessary
#' Plot the biomass of each species through time
#'
#' After running a projection, the biomass of each species can be plotted
#' against time. The biomass is calculated within user defined size limits (see
#' \code{\link{getBiomass}}). This plot is pretty easy to do by hand. It just
#' gets the biomass using the \code{\link{getBiomass}} method and plots using
#' the ggplot2 package. You can then fiddle about with colours and linetypes
#' etc. Just look at the source code for details.
#'
#' @param object An object of class \code{therMizerSim}.
#' @param start_time The first time step to be plotted. Default is the beginning
#' of the time series.
#' @param end_time The first time step to be plotted. Default is the end of the
#' time series.
#' @param print_it Display the plot, or just return the ggplot2 object. Default
#' value is TRUE
#' @param ... Other arguments to pass to \code{getBiomass} method, for example
#' \code{min_w} and \code{max_w}
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getBiomass}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotBiomass(sim)
#' plotBiomass(sim, min_w = 10, max_w = 1000)
#' }
setGeneric('plotBiomass', function(object, ...)
standardGeneric('plotBiomass'))
#' Plot the biomass using a \code{therMizerSim} object.
#' @rdname plotBiomass
setMethod('plotBiomass', signature(object='therMizerSim'),
function(object, print_it=TRUE, start_time=as.numeric(dimnames(object@n)[[1]][1]), end_time = as.numeric(dimnames(object@n)[[1]][dim(object@n)[1]]), ...){
b <- getBiomass(object, ...)
names(dimnames(b))[names(dimnames(b))=="sp"] <- "Species"
if(start_time >= end_time){
stop("start_time must be less than end_time")
}
b <- b[(as.numeric(dimnames(b)[[1]]) >= start_time) & (as.numeric(dimnames(b)[[1]]) <= end_time),,drop=FALSE]
bm <- melt(b)
# Force Species column to be a character (if numbers used - may be
# interpreted as integer and hence continuous)
bm$Species <- as.character(bm$Species)
# Due to log10, need to set a minimum value, seems like a feature in ggplot
min_value <- 1e-300
bm <- bm[bm$value >= min_value,]
p <- ggplot(bm) + geom_line(aes(x=time,y=value, colour=Species, linetype=Species)) + scale_y_continuous(trans="log10", name="Biomass") + scale_x_continuous(name="Time")
if (nrow(object@params@species_params)>12){
p <- ggplot(bm) + geom_line(aes(x=time,y=value, group=Species)) + scale_y_continuous(trans="log10", name="Biomass") + scale_x_continuous(name="Time")
}
if (print_it)
print(p)
return(p)
}
)
#' Plot the total yield of each species through time
#'
#' After running a projection, the total yield of each species across all
#' fishing gears can be plotted against time. This plot is pretty easy to do by
#' hand. It just gets the biomass using the \code{\link{getYield}} method and
#' plots using the ggplot2 package. You can then fiddle about with colours and
#' linetypes etc. Just look at the source code for details.
#'
#' @param object An object of class \code{therMizerSim}
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getYield} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getYield}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotYield(sim)
#' }
setGeneric('plotYield', function(object, ...)
standardGeneric('plotYield'))
#' Plot the yield using a \code{therMizerSim} object.
#' @rdname plotYield
setMethod('plotYield', signature(object='therMizerSim'),
function(object, print_it = TRUE, ...){
y <- getYield(object, ...)
names(dimnames(y))[names(dimnames(y))=="sp"] <- "Species"
ym <- melt(y)
p <- ggplot(ym) + geom_line(aes(x=time,y=value, colour=Species, linetype=Species)) + scale_y_continuous(trans="log10", name="Yield") + scale_x_continuous(name="Time")
if (nrow(object@params@species_params)>12){
p <- ggplot(ym) + geom_line(aes(x=time,y=value, group=Species)) + scale_y_continuous(trans="log10", name="Yield") + scale_x_continuous(name="Time")
}
if (print_it)
print(p)
return(p)
}
)
#' Plot the total yield of each species by gear through time
#'
#' After running a projection, the total yield of each species by fishing gear
#' can be plotted against time. This plot is pretty easy to do by hand. It just
#' gets the biomass using the \code{\link{getYieldGear}} method and plots using
#' the ggplot2 package. You can then fiddle about with colours and linetypes
#' etc. Just look at the source code for details.
#'
#' @param object An object of class \code{therMizerSim}
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getYieldGear} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getYieldGear}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotYieldGear(sim)
#' }
setGeneric('plotYieldGear', function(object, ...)
standardGeneric('plotYieldGear'))
#' Plot the yield of each gear using a \code{therMizerSim} object.
#' @rdname plotYieldGear
setMethod('plotYieldGear', signature(object='therMizerSim'),
function(object, print_it=TRUE, ...){
y <- getYieldGear(object, ...)
names(dimnames(y))[names(dimnames(y))=="sp"] <- "Species"
ym <- melt(y)
p <- ggplot(ym) + geom_line(aes(x=time,y=value, colour=Species, linetype=gear)) + scale_y_continuous(trans="log10", name="Yield") + scale_x_continuous(name="Time")
if (nrow(object@params@species_params)>12){
p <- ggplot(ym) + geom_line(aes(x=time,y=value, group=Species)) + scale_y_continuous(trans="log10", name="Yield") + scale_x_continuous(name="Time")
}
if (print_it)
print(p)
return(p)
}
)
#' Plot the abundance spectra of each species and the background population
#'
#' After running a projection, the spectra of the abundance of each species and
#' the background population can be plotted. The abundance is averaged over the
#' specified time range (a single value for the time range can be used to plot a
#' single time step). The abundance can be in terms of numbers or biomass,
#' depending on the \code{biomass} argument.
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param min_w Minimum weight to be plotted (useful for truncating the
#' background spectrum). Default value is a hundredth of the minimum size
#' value of the community.
#' @param biomass A boolean value. Should the biomass spectrum (TRUE) be plotted
#' or the abundance in numbers (FALSE). Default is TRUE.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments (currently unused)
#'
#' @return A ggplot2 object
#' @export
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotSpectra(sim)
#' plotSpectra(sim, min_w = 1e-6)
#' plotSpectra(sim, time_range = 10:20)
#' plotSpectra(sim, time_range = 10:20, biomass = FALSE)
#' }
setGeneric('plotSpectra', function(object, ...)
standardGeneric('plotSpectra'))
#' Plot the abundance spectra using a \code{therMizerSim} object.
#' @rdname plotSpectra
setMethod('plotSpectra', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), min_w =min(object@params@w)/100, biomass = TRUE, print_it = TRUE, ...){
time_elements <- get_time_elements(object,time_range)
spec_n <- apply(object@n[time_elements,,,drop=FALSE],c(2,3), mean)
background_n <- apply(object@n_pp[time_elements,,drop=FALSE],2,mean)
y_axis_name = "Abundance"
if (biomass){
spec_n <- sweep(spec_n,2,object@params@w,"*")
background_n <- background_n * object@params@w_full
y_axis_name = "Biomass"
}
# Make data.frame for plot
plot_dat <- data.frame(value = c(spec_n), Species = dimnames(spec_n)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
plot_dat <- rbind(plot_dat, data.frame(value = c(background_n), Species = "Background", w = object@params@w_full))
# lop off 0s in background and apply min_w
plot_dat <- plot_dat[(plot_dat$value > 0) & (plot_dat$w >= min_w),]
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = y_axis_name, trans="log10")
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = y_axis_name, trans="log10")
}
if (print_it)
print(p)
return(p)
}
)
#' Plot the feeding level of each species by size
#'
#' After running a projection, plot the feeding level of each species by size.
#' The feeding level is averaged over the specified time range (a single value
#' for the time range can be used).
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getFeedingLevel} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getFeedingLevel}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotFeedingLevel(sim)
#' plotFeedingLevel(sim, time_range = 10:20)
#' }
setGeneric('plotFeedingLevel', function(object, ...)
standardGeneric('plotFeedingLevel'))
#' PLot the feeding level using a \code{therMizerSim} object.
#' @rdname plotFeedingLevel
setMethod('plotFeedingLevel', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
feed_time <- getFeedingLevel(object=object, time_range=time_range, drop=FALSE, ...)
feed <- apply(feed_time, c(2,3), mean)
plot_dat <- data.frame(value = c(feed), Species = dimnames(feed)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Feeding Level", limits=c(0,1))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Feeding Level", limits=c(0,1))
}
if (print_it)
print(p)
return(p)
}
)
#' Plot M2 of each species by size
#'
#' After running a projection, plot M2 of each species by size. M2 is averaged
#' over the specified time range (a single value for the time range can be used
#' to plot a single time step).
#'
#' @param object An object of class \code{therMizerSim}
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getM2} method.
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getM2}}
#' @seealso \code{\link{getM2}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotM2(sim)
#' plotM2(sim, time_range = 10:20)
#' }
setGeneric('plotM2', function(object, ...)
standardGeneric('plotM2'))
#' Plot M2 using a \code{therMizerSim} object.
#' @rdname plotM2
setMethod('plotM2', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
m2_time <- getM2(object, time_range=time_range, drop=FALSE, ...)
m2 <- apply(m2_time, c(2,3), mean)
plot_dat <- data.frame(value = c(m2), Species = dimnames(m2)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "M2", limits=c(0,max(plot_dat$value)))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "M2", limits=c(0,max(plot_dat$value)))
}
if (print_it)
print(p)
return(p)
}
)
#' Plot total fishing mortality of each species by size
#'
#' After running a projection, plot the total fishing mortality of each species
#' by size. The total fishing mortality is averaged over the specified time
#' range (a single value for the time range can be used to plot a single time
#' step).
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getFMort} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getFMort}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotFMort(sim)
#' plotFMort(sim, time_range = 10:20)
#' }
setGeneric('plotFMort', function(object, ...)
standardGeneric('plotFMort'))
#' Plot total fishing mortality using a \code{therMizerSim} object.
#' @rdname plotFMort
setMethod('plotFMort', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
f_time <- getFMort(object, time_range=time_range, drop=FALSE, ...)
f <- apply(f_time, c(2,3), mean)
plot_dat <- data.frame(value = c(f), Species = dimnames(f)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Total fishing mortality", limits=c(0,max(plot_dat$value)))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Total fishing mortality", limits=c(0,max(plot_dat$value)))
}
if (print_it)
print(p)
return(p)
}
)
#' Plot total temperature effect on encounter rate on each species by size
#'
#' After running a projection, plot the temperature effect on encounter rate
#' for each species by size. The total temperature effect is averaged over
#' the specified time range (a single value for the time range can be used
#' to plot a single time step).
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getFMort} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getTempEffect}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotTempEffectEncount(sim)
#' plotTempEffectEncount(sim, time_range = 10:20)
#' }
setGeneric('plotTempEffectEncount', function(object, ...)
standardGeneric('plotTempEffectEncount'))
#' Plot total temperature effect using a \code{therMizerSim} object.
#' @rdname plotTempEffectEncount
setMethod('plotTempEffectEncount', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
te_time <- getTempEffectEncount(object, time_range=time_range, drop=FALSE, ...)
te <- apply(te_time, c(2,3), mean)
plot_dat <- data.frame(value = c(te), Species = dimnames(te)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Temperature Effect - Encounter", limits=c(0,max(plot_dat$value)))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Temperature Effect - Encounter", limits=c(0,max(plot_dat$value)))
}
if (print_it)
print(p)
return(p)
}
)
#' Plot total temperature effect on metabolism on each species by size
#'
#' After running a projection, plot the temperature effect on metabolism for
#' each species by size. The total temperature effect is averaged over the
#' specified time range (a single value for the time range can be used to
#' plot a single time step).
#'
#' @param object An object of class \code{therMizerSim}.
#' @param time_range The time range (either a vector of values, a vector of min
#' and max time, or a single value) to average the abundances over. Default is
#' the final time step.
#' @param print_it Display the plot, or just return the ggplot2 object
#' @param ... Other arguments to pass to \code{getFMort} method
#'
#' @return A ggplot2 object
#' @export
#' @seealso \code{\link{getTempEffect}}
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plotTempEffectMetab(sim)
#' plotTempEffectMetab(sim, time_range = 10:20)
#' }
setGeneric('plotTempEffectMetab', function(object, ...)
standardGeneric('plotTempEffectMetab'))
#' Plot total temperature effect using a \code{therMizerSim} object.
#' @rdname plotTempEffectMetab
setMethod('plotTempEffectMetab', signature(object='therMizerSim'),
function(object, time_range = max(as.numeric(dimnames(object@n)$time)), print_it = TRUE, ...){
te_time <- getTempEffectMetab(object, time_range=time_range, drop=FALSE, ...)
te <- apply(te_time, c(2,3), mean)
plot_dat <- data.frame(value = c(te), Species = dimnames(te)[[1]], w = rep(object@params@w, each=nrow(object@params@species_params)))
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, colour = Species, linetype=Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Temperature Effect - Metabolism", limits=c(0,max(plot_dat$value)))
if (nrow(object@params@species_params)>12){
p <- ggplot(plot_dat) + geom_line(aes(x=w, y = value, group = Species)) + scale_x_continuous(name = "Size", trans="log10") + scale_y_continuous(name = "Temperature Effect - Metabolism", limits=c(0,max(plot_dat$value)))
}
if (print_it)
print(p)
return(p)
}
)
#' Summary plot for \code{therMizerSim} objects
#'
#' After running a projection, produces 6 plots in the same window: feeding
#' level, predation mortality, fishing mortality, and temperature effects on
#' metabolism and encounter rate for each species by size; and biomass of
#' each species through time. This method just uses the other plotting
#' methods and puts them all in one window.
#'
#' @param x An object of class \code{therMizerSim}
#' @param y Not used
#' @param ... For additional arguments see the documentation for
#' \code{\link{plotBiomass}},
#' \code{\link{plotFeedingLevel}},\code{\link{plotM2}},
#' \code{\link{plotTempEffectEncount}},
#' \code{\link{plotTempEffectMetab}},
#' and \code{\link{plotFMort}}.
#' @return A viewport object
#' @export
#' @rdname plot_therMizer
#' @examples
#' \dontrun{
#' data(NS_species_params_gears)
#' data(inter)
#' params <- therMizerParams(NS_species_params_gears, inter)
#' sim <- project_therMizer(params, effort=1, t_max=20, t_save = 2)
#' plot(sim)
#' plot(sim, time_range = 10:20) # change time period for size-based plots
#' plot(sim, min_w = 10, max_w = 1000) # change size range for biomass plot
#' }
setMethod("plot", signature(x="therMizerSim", y="missing"),
function(x, ...){
p1 <- plotFeedingLevel(x,print_it = FALSE,...)
p2 <- plotBiomass(x,print_it = FALSE,...)
p3 <- plotM2(x,print_it = FALSE,...)
p4 <- plotFMort(x,print_it = FALSE,...)
p5 <- plotTempEffectEncount(x,print_it = FALSE,...)
p6 <- plotTempEffectMetab(x,print_it = FALSE,...)
grid.newpage()
glayout <- grid.layout(3,2) # widths and heights arguments
vp <- viewport(layout = glayout)
pushViewport(vp)
vplayout <- function(x,y)
viewport(layout.pos.row=x, layout.pos.col = y)
print(p1+ theme(legend.position="none"), vp = vplayout(1,1))
print(p2+ theme(legend.position="none"), vp = vplayout(1,2))
print(p3+ theme(legend.position="none"), vp = vplayout(2,1))
print(p4+ theme(legend.position="none"), vp = vplayout(2,2))
print(p5+ theme(legend.position="none"), vp = vplayout(3,1))
print(p6+ theme(legend.position="right", legend.key.size=unit(0.4,"cm")), vp = vplayout(3,2))
}
)
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