plot_run: Plot model simulations

In jrcunning/coRal: Dynamic bioenergetic modeling of coral-Symbiodinium symbioses

Description

The plot_run function will plot a multipanel figure with all model fluxes. Other functions can be used to plot single environmental factors or model fluxes independently.

Usage

plot_run(run)

plot_L(run, xlim = range(run$time), ylim = c(0, 60))

plot_DIN(run)

plot_gr(run)

plot_Hgr(
  run,
  xlim = range(run$time),
  ylim = c(min(0, min(run$H$dH.Hdt[-(1:10)])), max(run$H$dH.Hdt[-(1:10)]))
)

plot_sh(
  run,
  xlim = range(run$time),
  ylim = c(0, max(run$S$S/run$H$H, na.rm = T))
)

plot_Lq(run)

plot_photo(run)

plot_pl(run)

plot_PSU(run)

plot_ROS(run)

plot_symSU(run)

plot_sl(run)

plot_corSU(run)

plot_hl(run)

plot_bl(run)

plot_run_v2(run)

Arguments

run	The model simulation to plot from. This can be the object returned from run_coral or run_coral_ss.

Functions

• plot_L: Plot external irradiance

• plot_DIN: Plot external DIN concentration

• plot_gr: Plot specific growth rates of host and symbiont

• plot_Hgr: Plot specific growth rate of host

• plot_sh: Plot the symbiont to host biomass ratio

• plot_Lq: Plot light quenching (carbon fixation, NPQ, and excess (=ROS-producing))

• plot_photo: Plot photosynthesis rate (carbon fixation; jCP)

• plot_pl: Plot limitation coefficient for photosynthesis SU

• plot_PSU: Plot photosynthesis SU dynamics (proportions of light and CO2 rejected from SU)

• plot_ROS: Plot relative ROS production due to excitation energy in excess of carbon fixation and NPQ

• plot_symSU: Plot symbiont biomass SU dynamics (proportions of C and N rejected from SU)

• plot_sl: Plot symbiont biomass SU limitation coefficient

• plot_corSU: Plot host biomass SU dynamics (proportions of C and N rejected from SU)

• plot_hl: Plot host biomass SU limitation coefficient

• plot_bl: Plot both symbiont and host biomass SU limitation coefficients

• plot_run_v2: Plot another version of the multipanel run output

jrcunning/coRal documentation built on March 24, 2021, 1:28 a.m.