Goal of this vignette is to re-create figure 1C.
library(ggplot2) library(huisweis)
n_species <- 3 n_resources <- 3
Half-saturation constants for resources:
hsrs <- create_hsrs_1_a() knitr::kable(hsrs)
Species resource contents:
srcs <- create_srcs_1_a() 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()
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