scripts/07_phylogenetic_multinomial_model_and_extrapolation.R

In valerianoparravicini/Trophic_Fish_2020: Global gut content data synthesis and phylogeny delineate reef fish trophic guilds

library(caret)
library(fishualize)
library(tidyverse)
library(reshape)
library(lattice)
require(gridExtra) 
library(viridis)
library(parallel)
library(brms)
library(fishtree)
library(fishflux)
library(tidyverse)
library(parallel)
library(rfishbase)
library(ape)
library(picante)
library(rstan)
library(tidybayes)
library(ggnewscale)
library(tidytree)
library(ggtree)

Sys.setlocale("LC_MESSAGES", "en_US.utf8")


mod_predators <- readr::read_csv("output/results/mod_predators.csv")

devtools::load_all()

diet_cat <-  load_and_clean(mod_predators)

tree <- fishtree_complete_phylogeny(diet_cat$species)

dietcat <- modify_dietcat(diet_cat, tree)

delta_statistic <- delta_stat(dietcat)

fit_diet <- run_dietmodel(dietcat, tree)

r_phylo <- extract_r_phylo(fit_diet)
  
b <- extract_b(fit_diet)

extrap_test <- test_extrapolate(b, r_phylo, dietcat, tree)

extrapolation <- extrapolate(b, r_phylo)

delta_null <- delta_nullm(dietcat, n = 200)

adapt_extrapolation_cats(extrapolation)