CR_model: Simulate consumer-resource dynamics

Description Arguments Value Examples

View source: R/CR_model.R

Description

This function takes a named vector as initial community, simulates based on CR_ode function, and reports the output result matrix.

Arguments

community

the initial state of species and resource in a community. A named vector.

time_limit

time limit for ode.

time_step

time step for ode.

Value

a deSolve matrix

Examples

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# Load packages and example parameters
library(tidyverse)
library(deSolve)
data(example_parameter)

# Build regional species pool
pool_build()

# Create a community, a named vector
set.seed(1)
species <- sample(1:S_pool, S, replace = FALSE) %>% sort()
community <- 
  c(setNames(c(rep(1, P)), paste0("R", sprintf("%03d", 1:P))),
    setNames(c(rep(.1, length(species))), paste0("X", sprintf("%05d", species))))

# Run ode
result <- CR_model(community = community, time_limit = 100, time_step = 1)

# Plot
result %>%
 as.tibble() %>%
 gather("index", "value", -1) %>%
 ggplot(aes(x = time, y = value, color = index, lty = substr(index, 1, 1))) +
 geom_line() + 
 theme(legend.position="none")

Chang-Yu-Chang/MigrationCommunity documentation built on Sept. 8, 2018, 8:30 p.m.