nem_plot-ef-method: Visualizing the energy structure of nematode communities...

In easynem: Nematode Community Analysis

Visualizing the energy structure of nematode communities (single factor)

Description

The nem_plot function is generalized to the ef-class and is used to visualize the energy structure of nematode communities. a five-node food web was constructed with bacterivores, fungivores and herbivores receiving energy from basal resources (R), omnivores-carnivores receiving energy from other nodes. Numbers along the lines represented energy flux (ug C / 100 g dry soil / day). The size of nodes corresponds to the fresh biomass (ug / 100 g dry soil). Uniformity (U) of soil nematode energetic structure (unitless, mean ± standard error) was calculated as the ratio of the mean of summed energy flux through each energy channel to the standard deviation of these mean values.

Usage

## S4 method for signature 'ef'
nem_plot(object)

Arguments

object

A ef-class object.

Details

To facilitate code interpretation, it is recommended to use the pipe symbol |> to connect functions:

nem_plot <- nem |> calc_nemindex() |> calc_ef(Treatments) |> nem_plot()

Value

An gg or ggplot object.

References

• Wan, Bingbing, et al. "Organic amendments increase the flow uniformity of energy across nematode food webs." Soil Biology and Biochemistry 170 (2022): 108695.

• Ferris, H., 2010. Form and function: metabolic footprints of nematodes in the soil food web. European Journal of Soil Biology 46, 97–104.

• Van Den Hoogen, Johan, et al. "Soil nematode abundance and functional group composition at a global scale." Nature 572.7768 (2019): 194-198.

• Barnes, A.D., Jochum, M., Mumme, S., Haneda, N.F., Farajallah, A., Widarto, T.H., Brose, U., 2014. Consequences of tropical land use for multitrophic biodiversity and ecosystem functioning. Nature Communications 5, 1–7.

• De Ruiter, P.C., Van Veen, J.A., Moore, J.C., Brussaard, L., Hunt, H.W., 1993. Calculation of nitrogen mineralization in soil food webs. Plant and Soil 157, 263–273.

See Also

The nem_plot() is used to visualize the calculation results and is a generalized function for multiple classes including beta-class, beta2-class, compare-class, compare2-class, ef-class, ef2-class, funguild-class, funguild2-class, mf-class, mf2-class, ter-class, ter2-class, etc.

Examples

nem <- read_nem2(tab = nemtab, tax = nemtax, meta = nemmeta)
nem_plot <- nem |>
            calc_nemindex() |>
            calc_ef(Treatments) |>
            nem_plot()
nem_plot

easynem documentation built on Nov. 5, 2025, 7:39 p.m.