rundeb: rundeb

In mrke/NicheMapR: R implementation of Niche Mapper software for biophysical modelling

rundeb

Description

Function to simulate the development, growth and reproduction trajectory of an organism using DEB theory, drawing parameters from the 'AmP' parameter database at https://github.com/add-my-pet/AmPtool. It requires the 'allStat.mat' file to have been converted to 'allStat.Rda' via the R.matlab package (i.e. allStat <- readMat('allStat.mat' then save(allStat, file = 'allstat.Rda'))).

Usage

rundeb(
  allstat = allstat,
  species = "Daphnia.magna",
  Euler = 0,
  start.stage = 0,
  stages = 6,
  S_instar = rep(1.618, stages),
  ndays = 50,
  div = 24,
  starve_mode = 1,
  Tbs = rep(20, ndays * div),
  Xs = rep(100, ndays * div),
  E_sm = 350,
  fdry = 0.3,
  clutchsize = 5,
  kap.mult = 1,
  z.mult = 1,
  v.mult = 1,
  p.M.mult = 1,
  E.0.mult = 1,
  plot = 1,
  mass.unit = "g",
  length.unit = "cm",
  ageing = 1
)

Arguments

allstat	= allstat, the allstat data set
species	= 'Daphnia.magna', a species in the allstat file
Euler	= 0, use Euler integration? (faster, but less accurate), 0 or 1
start.stage	= 0, stage at which simulation starts, 0=embryo, 1=birth, 2=puberty
stages	= 6, how many life cycle stages? (e.g. 6 for a abp insect model), #
S_instar	= rep(1.618, stages), 'stress' factor determining body lengths at which molts occur (for abp insect model), -
ndays	= 50, days to run the simulation for
div	= 24, value to divide the default step size (days) by, which determines output frequency (and integration frequency if Euler = 1)
Tbs	= rep(20, ndays*div), vector of body temperatures for each time step, °C
Xs	= rep(100, ndays*div), vector of food densities,J/cm2 or J/cm3
E_sm	= 350, maximum stomach energy density per structure, J/cm3
fdry	= 0.3, dry fraction of food, -
clutchsize	= 5, eggs in a clutch, #
kap.mult	= 1, multiplier on original value for kappa, -
z.mult	= 1, multiplier on original value of z, to explore implications of DEB covariation rules for body size scaling, -
v.mult	= 1, multiplier on original value of energy conductance, v, -
p.M.mult	= 1, multiplier on original value of somatic maintenance p.M, -
E.0.mult	= 1, multiplier on original value of egg energy E.0, -
plot	= 1, produce example plots? 0=no, 1=yes
mass.unit	= 'g', mass unit for the plots, 'mg', 'g' or 'kg'
length.unit	= 'cm', length unit for the plots, 'mm', 'cm' or 'm'
ageing	= 1, impose ageing? 0=immortal, 1=aging according to parameter h.a

Examples

#library(R.matlab)
#allStat<-readMat('allStat.mat') # this will take a few minutes
#save(allStat, file = 'allstat.Rda') # save it as an R data file for faster future loading
load('allStat.Rda')
species <- "Daphnia.magna" # must be in the AmP collection - see allDEB.species list
Euler <- 0 # use Euler integration (faster but less accurate) (1) or deSolve's ODE solve (0)
start.stage <- 0 # stage in life cycle to start (0 = egg, 1 = juvenile, 2 = puberty)
ndays <- 50 # number days to run the simulation for
div <- 24 # time step divider (1 = days, 24 = hours, etc.) - keep small if using Euler method for integration
starve_mode <- 1 # Determines how reproduction buffer is used during starvation, where 0 means it is not used, 1 means it is used before structure is mobilised and 2 means it is used to maximise reserve density
Tbs <- rep(20, ndays * div) # deg C, body temperature
starvetime <- 0 # length of low food period when simulating starvation
X <- 100 # J/cm2 base food density
Xs <- c(rep(X, ndays * div/2), rep(0.000005, starvetime), rep(X, ndays * div/2-starvetime + 1)) # body temperature
E_sm <- 350 # J/cm3, volume-specific stomach energy
fdry <- 0.3 # J/cm3, volume-specific stomach energy
clutchsize <- 50 # -, clutch size
kap.mult <- 1 # -, factor to multiply kappa by (caps at 1)
p.M.mult <- 1 # -, factor to multiply p.M by (caps at 1)
v.mult <- 1 # -, factor to multiply energy conductance by
z.mult <- 1 # -, factor to multiply zoom factor by
E.0.mult <- 1 # -, factor by which to multiply initial egg energy
plot <- 1 # plot results?
mass.unit <- 'g'
length.unit <- 'mm'

deb <- rundeb(species = species, ndays = ndays, div = div, starve_mode = starve.mode, Tbs = Tbs,
              clutchsize = clutchsize, kap.mult = kap.mult, v.mult = v.mult,
              p.M.mult = p.M.mult, Xs = Xs, z.mult = z.mult, E.0.mult = E.0.mult,
              mass.unit = mass.unit, length.unit = length.unit, start.stage = start.stage,
              E_sm = E_sm, Euler = Euler, plot = plot)

debout <- as.data.frame(deb$debout) # retrieve the output
parameters <- deb$pars # retrieve the extracted parameters

mrke/NicheMapR documentation built on April 3, 2024, 10:05 a.m.