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RavRK_4_results.R
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RavRK_4_results.R
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##---------------------------------------------------------------------------------
##
## Code to reproduce analyses from the manuscript:
## “Roadkill islands: carnivore extinction shifts seasonal use of roadside carrion
## by generalist avian scavenger” by Fielding, Matthew; Buettel, Jessie C; Brook,
## Barry; Stojanović, Dejan; Yates, Luke (2021)
##
##
## This script produce interval plots of MCMC results
## Figure 5 - Parameter estimates on the log-linear scale.
##
## Authors: L Yates, M Fielding
## Date: 01/07/2020
##
##---------------------------------------------------------------------------------
#library(spatstat)
library(tidyverse)
library(pbmcapply)
library(ggpubr)
library(broom)
library(rstanarm)
library(shinystan)
library(bayesplot)
rm(list=ls())
m.re.nest.diag <- readRDS("results/m.re.nest.diag_longRun_2021_02_09.rds")
seasons <- c(spring = "spring", summer = "summer", autumn = "autumn", winter = "winter")
#-------------
# Prepare data
#-------------
m.df <- m.re.nest.diag %>% as.data.frame() %>% as_tibble()
# RK.dist (X_R) data
# account for treatment contrast to calculate seasonal intercepts
RK.df <- m.df %>% select(contains("RK.dist")) %>%
mutate(spring = `seasonspring:RK.dist` + RK.dist, `seasonspring:RK.dist` = NULL) %>%
mutate(summer = `seasonsummer:RK.dist` + RK.dist, `seasonsummer:RK.dist` = NULL) %>%
mutate(winter = `seasonwinter:RK.dist` + RK.dist, `seasonwinter:RK.dist` = NULL) %>%
mutate(autumn = RK.dist, RK.dist = NULL) %>%
select(-contains("sigma")) %>%
rename_at(vars(starts_with("b")), function(x) str_remove(x,fixed("b[RK.dist season:route:")) %>% str_remove(fixed("]")))
RK.sr <- lapply(seasons, function(seas) select(RK.df,contains(paste0(seas,":"))) %>%
mutate_all(function(x) x + RK.df[[seas]]) %>%
rename_all(~str_remove(., fixed(paste0(seas,":")))) %>%
gather("route","estimate")) %>% bind_rows(.id = "season")
# unlogged scale (multiplicative form)
#RK.sr.exp <- RK.sr %>% mutate(estimate = exp(estimate/attributes(m.re.nest.diag$data$RK.dist)$`scaled:scale`))
# O.dist (X_F) data
# account for treatment contrast to calculate seasonal intercepts
m.df %>% select(contains("O.dist")) %>% names
O.df <- m.df %>% select(contains("O.dist")) %>%
mutate(spring = `O.dist:seasonspring` + O.dist, `O.dist:seasonspring` = NULL) %>%
mutate(summer = `O.dist:seasonsummer` + O.dist, `O.dist:seasonsummer` = NULL) %>%
mutate(winter = `O.dist:seasonwinter` + O.dist, `O.dist:seasonwinter` = NULL) %>%