# !diagnostics off knitr::opts_chunk$set(cache = T, echo = F) library(micro.crm) library(tidyverse) library(igraph) library(data.table)
This script includes the following steps:
Incoluation from pool
Read the final time step
```{bash eval = F}
Rscript self-assembly.R migration-size001
# Read files from the community ```r rm(list=ls()) treatment_name <- "migration-size001" parameter_load(parameter_text = paste0("parameter_script/", treatment_name, ".txt")) pool_build() # Community result <- result_read(dir = "simulation_result/", pattern = treatment_name, threshold = threshold)
After reading the individual files and the equilibrium is saved.
f <- list.files("simulation_result/equilibrium/") %>% grep("migration-size", ., value = T) parameter_treatment <- parameter_read(f, "simulation_result/equilibrium/") %>% select(-function_group, -replicate)
result_equilibrium <- lapply(f, function(x) fread(paste0("simulation_result/equilibrium/", x))) %>% do.call("rbind", .) %>% left_join(parameter_treatment, by = "treatment") result_equilibrium <- result_equilibrium %>% group_by(treatment, replicate) %>% mutate(biomassTotal = sum(value), valueStandard = value / biomassTotal) result_equilibrium %>% ungroup() %>% # filter(treatment == "migration-size001") %>% distinct(treatment, variable) %>% arrange(treatment, variable) %>% group_by(treatment) %>% summarize(n())
p3 <- result_equilibrium %>% select(variable, valueStandard, function_group, treatment, replicate) %>% mutate(value = valueStandard) %>% select(-valueStandard) %>% group_by(treatment, replicate) %>% split.data.frame(f = .$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()
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