5.5. Plotting outputs

Plotting Osmose outputs is achieved by calling the generic plot function on the osmose object, output by the read_osmose function. The function takes as argument the variable to be displayed (what argument). The species argument allows to specify the indexes of the species to display (cf. the X in the species.name.spX parameters).

library("osmose")
getwd()

input.dir = file.path("astart", "_static", "gog_v4", "output")
data = read_osmose(input.dir)

output.dir = file.path("rosmose", "_static")

test = getVar(data, "species")

png(file=file.path(output.dir, "biomass.png"))
plot(data, what="biomass")

png(file=file.path(output.dir, "abundance.png"))
plot(data, what="abundance", species=c(0, 1, 2))

png(file=file.path(output.dir, "yield.png"))
plot(data, what="yield")

png(file=file.path(output.dir, "yieldN.png"))
plot(data, what="yieldN")

Hint

When several replicates are run, the uncertainty due to the stochastic mortality is displayed as a grey shading.

Warning

At this time, only these four variables can be plotted. However, more plot functions (diet matrix, mortality, etc.) will be released soon.

../_images/biomass.png

Fig. 5.4 Biomass plot

../_images/abundance.png

Fig. 5.5 Abundance plot

../_images/yield.png

Fig. 5.6 Yield biomass plot

../_images/yieldN.png

Fig. 5.7 Yield abundance plot