Goal of this vignette is to re-create figure 1C.

Setup

library(ggplot2)
library(huisweis)

Constants

n_species <- 6
n_resources <- 3

Half-saturation constants for resources:

hsrs <- create_hsrs_1_c()
knitr::kable(hsrs)

Species resource contents:

srcs <- create_srcs_1_c()
knitr::kable(srcs)
supply_rates <- get_supply_rates()
print(supply_rates)
initial_resource_densities <- supply_rates
print(initial_resource_densities)
initial_species_densities <- create_init_spec_densities(n_species = n_species)
print(initial_species_densities)
max_growth_rates <- get_max_growth_rates(n_species = n_species)
mortality_rates <- get_mortality_rates(n_species = n_species)
print(mortality_rates)
turnover_rate <- get_turnover_rate()
print(turnover_rate)
t_max <- 100
print(t_max)
dt <- 0.01
print(dt)
df <- run_sim(
  initial_species_densities = initial_species_densities,
  initial_resource_densities = initial_resource_densities,
  dt = dt,
  t_max = t_max,
  max_growth_rates = max_growth_rates,
  mortality_rates = mortality_rates,
  hsrs = hsrs,
  srcs = srcs,
  supply_rates = supply_rates,
  turnover_rate = turnover_rate
)
knitr::kable(head(df))
df_long <- reshape2::melt(df, id = "t")
knitr::kable(head(df_long))
names(df_long)
ggplot(data = df_long, aes(x = t, y = value, fill = variable)) + geom_line()


richelbilderbeek/huisweis documentation built on May 9, 2019, 7:36 a.m.