A function to calculate carbon and nitrogen fluxes in the food web.
comana(
usin,
mkplot = FALSE,
whattoplot = c("web", "Nmin", "Cmin"),
showCN = FALSE,
BOX.SIZE = 0.1,
BOX.PROP = 0.3,
BOX.CEX = 1,
PLOT.CEX = 1,
edgepos = c(0.1, 0.9),
TCK = 0.05,
shuffleTL = FALSE,
prettynames = NA,
fwdlwdcust = NULL,
arrowlog = FALSE,
arrowsizerange = c(0.1, 30),
rmzeros = TRUE,
eqmtolerance = NA
)A list of consumption rates, carbon mineralization, nitrogen mineralization, carbon and nitrogen consumption rates, and the modified community if zeros where removed or sorting occurred.
The community that you are analyzing: contains a matrix of interactions and a data frame of properties in a list.
Boolean: Should the plots be output?
A vector of what to plot. Food web typology (web), nitrogen mineralization (Nmin), and/or carbon mineralization (Cmin).
Boolean: # Should the food web show the C:N ratio of each trophic species next to it's name in the food web plot?
Size of boxes in the food web plot
Proportion of box length and width in the food web plot
Size of box text in the food web plot
Size of plot
Where to put the far left and far right boxes for trophic species in the food web plot (range = 0, 1).
The size of the ticks on the C.min and N.min plots.
A Boolean stating whether the community should be sorted.
Alternative names in order for the food web plot trophic species. Cannot be used if showCN = T.
# A matrix of arrow line widths, same dimensions at the food web for plot customization.
Boolean: Should relative arrow widths in the food web plot be on a log scale?
The range of arrow sizes in the food web plot.
A Boolean determining whether trophic species with zero biomass should be removed from the community before analysis.
A value used to set the equilibrium tolerance for the food web verification. If NA, the default value used by the function all.equal is used, which is approximately 1.5e-8.