comana {soilfoodwebs}

A function to calculate carbon and nitrogen fluxes in the food web.

Description

A function to calculate carbon and nitrogen fluxes in the food web.

Usage

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
)

Arguments

usin

The community that you are analyzing: contains a matrix of interactions and a data frame of properties in a list.

mkplot

Boolean: Should the plots be output?

whattoplot

A vector of what to plot. Food web typology (web), nitrogen mineralization (Nmin), and/or carbon mineralization (Cmin).

showCN

Boolean: # Should the food web show the C:N ratio of each trophic species next to it's name in the food web plot?

BOX.SIZE

Size of boxes in the food web plot

BOX.PROP

Proportion of box length and width in the food web plot

BOX.CEX

Size of box text in the food web plot

PLOT.CEX

Size of plot

edgepos

Where to put the far left and far right boxes for trophic species in the food web plot (range = 0, 1).

TCK

The size of the ticks on the C.min and N.min plots.

shuffleTL

A Boolean stating whether the community should be sorted.

prettynames

Alternative names in order for the food web plot trophic species. Cannot be used if showCN = T.

fwdlwdcust

# A matrix of arrow line widths, same dimensions at the food web for plot customization.

arrowlog

Boolean: Should relative arrow widths in the food web plot be on a log scale?

arrowsizerange

The range of arrow sizes in the food web plot.

rmzeros

A Boolean determining whether trophic species with zero biomass should be removed from the community before analysis.

eqmtolerance

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.

Value

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.

Examples

comana(intro_comm)