In Chang-Yu-Chang/MigrationCommunity: Microbial Consumer-Resource Model

# !diagnostics off
knitr::opts_chunk$set(cache = T, echo = F)
library(micro.crm)
library(tidyverse)
library(igraph)
library(data.table)

This script includes the following steps:

1. Incoluation from pool

2. Read the final time step

Simulation

```{bash eval = F}

Self-assembly

Rscript self-assembly.R migration-size001

# Read files from the community 

```r
rm(list=ls())
treatment_name <- "migration-size001"
parameter_load(parameter_text = paste0("parameter_script/", treatment_name, ".txt"))
pool_build()

# Community
result <- result_read(dir = "simulation_result/", pattern = treatment_name, threshold = threshold)

After reading the individual files and the equilibrium is saved.

f <- list.files("simulation_result/equilibrium/") %>% grep("migration-size", ., value = T)
parameter_treatment <- parameter_read(f, "simulation_result/equilibrium/") %>%
  select(-function_group, -replicate)

result_equilibrium <- 
  lapply(f, function(x) fread(paste0("simulation_result/equilibrium/", x))) %>%
  do.call("rbind", .) %>%
  left_join(parameter_treatment, by = "treatment")

result_equilibrium <- result_equilibrium %>%
  group_by(treatment, replicate) %>%
  mutate(biomassTotal = sum(value), 
         valueStandard = value / biomassTotal)

result_equilibrium %>% 
  ungroup() %>% 
#  filter(treatment == "migration-size001") %>%
  distinct(treatment, variable) %>%
  arrange(treatment, variable) %>%
  group_by(treatment) %>%
  summarize(n())

p3 <- result_equilibrium %>% select(variable, valueStandard, function_group, treatment, replicate) %>%
  mutate(value = valueStandard) %>% select(-valueStandard) %>%
  group_by(treatment, replicate) %>%
  split.data.frame(f = .$treatment) %>%
  lapply(beta_diversity) %>%
  rbindlist() %>% 
  mutate(treatment = paste0("migration-size", sprintf("%03d", 1:5))) %>%
  left_join(select(parameter_treatment, I, treatment), by = "treatment")  %>%
  ggplot(aes(x = I, y = mean)) +
  geom_point() + geom_segment(aes(x = I, xend = I, y = min(mean + 2*sd, 1), yend = mean - 2*sd)) +
  theme_bw() +
  labs(x = "inocula size of initial community", y = "beta diversity") +
  ggtitle("No migration")

p3
pdf("figure/beta-diversity_migration-size.pdf"); p3; dev.off()

Chang-Yu-Chang/MigrationCommunity documentation built on Aug. 13, 2019, 9:41 p.m.