In quantifish/influ2: Influence plots

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Introduction

Hurdle models are tricky, heres how to do it.

library(tidyverse)
library(reshape2)
library(brms)
library(influ2)
library(bayesplot)

options(mc.cores = parallel::detectCores())

# Simulate some data to use
set.seed(2020)

# create data according to the hurdle-lognormal distribution
pi <- 0.3 # probability of a zero
mu_log <- 2 # lognormal mean
sigma_log <- 0.2

# generate data
N <- 1000

set.seed(seed = 42)
ydf <- data.frame(year = 1995:2015, value = rnorm(n = 21, mean = 0, sd = 1))
idy <- sample(x = 1:21, size = N, replace = TRUE)
yr <- ydf[idy,]
levs <- sample(x = c("treat", "placebo"), size = N, replace = TRUE)
group <- data.frame(level = levs) %>% 
  mutate(value = ifelse(level == "treat", 0.9, 0))
y <- (1 - rbinom(n = N, size = 1, prob = pi)) * 
  rlnorm(n = N, meanlog = mu_log + group$value + yr$value, sdlog = sigma_log)
sim_data <- data.frame(y = y, group = group$level, year = factor(yr$year))

head(sim_data)

plot_bubble(df = sim_data, group = c("year", "group"))

m1 <- brm(bf(y ~ year + group, hu ~ 1), 
          data = sim_data, family = "hurdle_lognormal", chains = 2, 
          file = "m1", file_refit = "never")

plot_index(m1, year = "year")

# plot_influ(m1, year = "year")

# plot_bayesian_cdi(fit = m1, xfocus = "group", yfocus = "year", xlab = "Group")

quantifish/influ2 documentation built on Dec. 14, 2024, 5:10 a.m.