This method takes a osmose object to make useful plot
for each variables.
# S3 method for osmose
plot(x, type = "biomass", ...)Object of osmose class (see the read_osmose function).
Name of the variable to plot. By default is type = "biomass" but
it could be:
"biomass" to plot the species biomass.
"abundance" to plot the species abundance.
"yield" to plot the species yield.
"yieldN" to plot the species yield (in numbers).
Extra arguments of the function. These could be:
aggregate A logical parameter. By default aggregate = FALSE
show the evolution of the variable over the time. aggregate = TRUE show
the aggregation of the variable for each species.
start A number to indicate the first x-axis element to plot when
aggregate = FALSE. By default start = NULL and start with the
first element of the osmose object over the time.
conf A number to indicate the confidence interval to plot. By default
conf = 0.95.
factor A number to indicate the variable scale on the y axis. By default
factor = 1e-6.
replicates A logical parameter. replicates = FALSE show the
mean value of the variable over the time but replicates = TRUE show the
values obtained in each replicates of the osmose object.
nrep A number to indicate the number of replicates to show. This
parameter is used only when replicates = TRUE. By default nrep = 3.
col The color of the lines (agregate = FALSE),
barplot (for variables biomass or abundance using aggregate = TRUE) or
boxplot (for variables yield or yieldN using aggregate = TRUE).
By default col = "black".
alpha A number between 0 and 1. Indicate the transparency with which the
confidence interval is colored. By default alpha = 0.5.
A graph of a osmose object.
The parameters: start, conf, factor,
replicates, nrep, alpha are used only when aggregate = FALSE.
When aggregate = TRUE a barplot is generated for the
variables "biomass" and "abundance". Each bar of the barplot represents the
average value of the variable over the time for each species. For the variables
"yield" and "yieldN" a boxplot is generated. Each box of the boxplot
represents one species.
The plots with the evolution of the variable over the time (aggregate = FALSE)
show the variable of each species included in a osmose object, where the x axis
represents the time and the y axis the variable. The line (by default a black line)
is the mean value over the time and the light grey part represent the confidence
interval (by default conf = 0.95).