In diazrenata/scadsplants: Constraints on SADs of Portal Plants

knitr::opts_chunk$set(echo = TRUE)
library(drake)
library(dplyr)
library(ggplot2)

  all_dat <- portalr::plant_abundance(level = "Treatment", type = "Annuals", plots = "All", unknowns = F, correct_sp = T, shape = "flat", min_quads = 16) %>%
    dplyr::filter(treatment == "control") %>%
    dplyr::select(year, species, abundance, season) %>%
    dplyr::rename(abund = abundance) %>%
  dplyr::group_by(year, season) %>%
  dplyr::arrange(abund) %>%
    dplyr::mutate(rank = dplyr::row_number()) %>% 
  dplyr::ungroup() %>%
  dplyr::select(-species) %>%
  dplyr::mutate(sim = -99,
                  source = "observed")


all_dat <- all_dat %>%
  group_by(year, season) %>%
  summarize(nspp = max(rank),
            nind = sum(abund)) %>%
  ungroup()

statevar_plot <- ggplot(data = all_dat, aes(x = nspp, y = nind, label = year, color = season)) +
  geom_label() +
  theme_bw() +
  scale_color_viridis_d(end = .6)

statevar_plot

nind_hist <- ggplot(data = all_dat, aes(x = nind)) +
  geom_density() +
  theme_bw()

nind_hist


nspp_hist <- ggplot(data = all_dat, aes(x = nspp)) +
  geom_density() +
  theme_bw()

nspp_hist

small_years <- all_dat %>%
  filter(nspp <= 40,
         nind <= 15000) %>%
  group_by(year) %>%
  summarize(nb_seasons = n()) %>%
  ungroup() %>%
  filter(nb_seasons == 2)

small_years_dat <- all_dat %>%
  filter(year %in% small_years$year)

small_statevar_plot <- ggplot(data = small_years_dat, aes(x = nspp, y = nind, label = year, color = season)) +
  geom_label() +
  theme_bw() +
  scale_color_viridis_d(end = .6)

small_statevar_plot

small_years_dat