test_that("simple model", { # data("Mallard_Atrazine") # atrazine <- Mallard_Atrazine[1:3] # keep only the data.frames # atrazine <- lapply(atrazine, function(d){ # d$repl = paste(d$repl, d$conc, sep = "_") # return(d) # }) # atrazine <- prep_food_data(atrazine, interactive = FALSE, default_remove = TRUE) # data_egg <- atrazine$D_eggs # empty_first_time <- (data_egg$time == min(data_egg$time) & data_egg$n_egg == 0) # data_egg[empty_first_time & !is.na(empty_first_time),]$n_egg <- 10e-6 # fit_args <- list( # t_s = 50, # t_end = max(atrazine$D_eggs$time), # W_B0 = 10, # food_data = atrazine$D_food, # weight_data = atrazine$D_weight, # egg_data = data_egg # ) # simpleData <- model_data(fit_args) # # fit <- fit(as.birdKISSdata(simpleData), iter = 100, chains = 1) # # ext = rstan::extract(fit, pars = c("Ww_sim", "R_sim")) # Ww_sim = apply(ext$Ww_sim, 2, quantile, probs = 0.5) # R_sim = apply(ext$R_sim, 2, quantile, probs = 0.5) # # d = simpleData # plot(d$tX, d$Ww) # points(d$tX, Ww_sim, col = "red", pch = 3) # # plot(d$tX, d$R) # points(d$tX, R_sim, col = "red", pch = 3) })