ProvidenciaChemo:

library(tidyverse)

ring <- read_csv(here::here("data","Fruc_ring.csv")) %>%
  mutate(food = fct_relevel(food, "OP50"),
         plate = factor(seq(1:nrow(.))),
         fraction_out =  Nout/Ntotal)

ring %>%
  filter(odorant == "none",
         #food %in% c("OP50", "JUb39"),
         genotype == "N2",
         ring == "3M fructose") %>%
  ggplot(aes(x = food, y = fraction_out)) +
  ggbeeswarm::geom_quasirandom(aes(color = date)) +
  #scale_color_plot(palette = "2-Ps", drop = TRUE) +
  #theme_black() +
  stat_summary(aes(y=fraction_out),
               fun.y = median,
               fun.ymin = median,
               fun.ymax = median,
               geom = "crossbar",
               width = 0.5,
               lwd = 0.35,
               colour = "black") +
  facet_grid(~genotype) +
  guides(colour = FALSE) +
  #add.n(food) +
  add.quartiles(fraction_out)

#### glycerol data ####
  glycerol <- read_csv(here::here('extdata/Figure_S1a.csv'))
    mutate(food = fct_relevel(food, "OP50"))




#singular fit

  lme4::glmer(data = glycerol, cbind(Nout, Ntotal - Nout) ~ food + (1|plate) + (1|date), family = "binomial") %>% summary()

  lm(data = glycerol, fraction_out ~ food) %>% summary()

stan_mod <- rstanarm::stan_glmer(data = glycerol, cbind(Nout, Ntotal - Nout) ~ food + (1|plate) + (1|date), family = "binomial",
                    seed = 6459,
                    chains = 4,
                    cores = 4,
                    adapt_delta = 0.99)

fitted <- stan_mod %>%
  emmeans::emmeans(~food) %>%
  coda::as.mcmc() %>%
  bayesplot::mcmc_intervals_data(transformations = function(x) boot::inv.logit(x)) %>%
  mutate(food = factor(c("OP50", "JUb39"), levels = c("OP50", "JUb39")))

glycerol  %>%
  ggplot(aes(y = fraction_out, x = factor(1))) +
  ggbeeswarm::geom_quasirandom(aes(color = food), width = 0.1) +
  scale_color_plot(palette = "2-Ps", drop = TRUE) +
  #theme_black() +
  add.mean(fraction_out, colour = "red", width = 0.1) +
  stat_summary(fun.data = mean_se,
               geom = "errorbar",
               width = 0.2,
               lwd = 0.35,
               colour = "black") +
  facet_grid(~food) +
  guides(colour = FALSE) +
  add.n(1, y.pos = -0.1) +
  coord_cartesian(ylim = c(-.1, 1)) +
  geom_crossbar(data = fitted,
                aes(x = 1.4,
                    y = m,
                    ymin = m,
                    ymax = m),
                width = 0.05,
                colour = "darkgrey") +
  geom_pointrange(data = fitted,
                  aes(x =1.4,
                      y = m,
                      ymin = ll,
                      ymax = hh),
                  size = 0.5,
                  fatten = 0,
                  color = "darkgrey") +
  geom_pointrange(data = fitted,
                  aes(x = 1.4,
                      y = m,
                      ymin = l,
                      ymax =h),
                  size = 1, fatten = 0,
                  colour = "darkgrey")