Disturbance Genus

Code

data <- read_tsv("../modelling/data/derived_data/data_rec.tsv", col_types = cols()) %>%
    select(-y) %>% 
    filter(variable %in% c("ba", "diversity_q1_gen")) %>%
    select(-sitenum, -plotnum) %>% 
    pivot_wider(names_from = variable, values_from = value) %>% 
    na.omit() %>% 
    filter(!(site %in% c("Manare", "Montagne Tortue", "Nelliyampathy",
                         "Uppangala", "BAFOG", "Sao Nicolau",
                         "Kabo", "Mil", "Corinto", "Jenaro Herrera",
                         "Peixoto", "Iwokrama", "Antimary", "Peteco")))
trajectories <- read_tsv("chains/dist-diversity_q1_gen-trajectories.tsv")
parameters <-  read_tsv("chains/dist-diversity_q1_gen-parameters.tsv")
area <- data %>%
  select(site, plot, area) %>% 
  unique() %>% 
  group_by(site) %>% 
  summarise(area = mean(area))
filter(parameters, variable == "gamma") %>% 
  left_join(area) %>% 
  ggplot(aes(median, reorder(site, median, decreasing = TRUE))) +
  geom_vline(xintercept = 0, col = "darkgrey") +
  geom_segment(aes(x = (median - sd),
                   xend = (median + sd))) +
  geom_segment(aes(x = q5, xend = q95), size = .1) +
  geom_point() +
  geom_text(aes(label = paste(round(area, 1), "ha")), nudge_y = .5, size = 2) +
  theme_bw() +
  scale_x_continuous(expression(gamma~"["~"%"~"%"^{-1}~"]")) +
  ylab("") +
  scale_color_viridis_c()

Posterior of the parameter gamma representing basal are disturbance intensity effect on genus diversity short term increase

Code

read_tsv("chains/joint-diversity_q1_gen-parameters.tsv") %>% 
  filter(variable == "gamma") %>% 
  left_join(filter(parameters, variable == "gamma") %>% 
              select(site, median, sd, q5, q95) %>% 
              rename(median_new = median, sd_new = sd,
                     q5_new = q5, q95_new = q95)
  ) %>% 
  filter(!is.na(median_new)) %>% 
  ggplot(aes(-median, median_new)) +
  geom_hline(yintercept = 0, col = "grey") +
  geom_vline(xintercept = 0, col = "grey") +
  geom_point() +
  geom_segment(aes(x = -median - sd, xend = -median + sd)) +
  geom_segment(aes(x = -q5, xend = -q95), size = .1) +
   geom_segment(aes(y = median_new - sd_new, yend = median_new + sd_new)) +
  geom_segment(aes(y = q5_new, yend = q95_new), size = .1) +
  ggrepel::geom_text_repel(aes(label = site)) +
  theme_bw() +
  geom_abline() +
  ggpubr::stat_cor() +
  xlab("gamma from joint modelling") +
  ylab("gamma from observed disturbance")

Comparison with joint inference of genus order 1 diversity and basal area.