Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 6
)
## ----setup--------------------------------------------------------------------
library(biogrowth)
library(tidyverse)
library(cowplot)
## -----------------------------------------------------------------------------
data("example_dynamic_growth")
data("example_env_conditions")
sec_models <- list(temperature = "CPM", aw = "CPM")
known_pars <- list(Nmax = 1e4, # Primary model
N0 = 1e0, Q0 = 1e-3, # Initial values of the primary model
mu_opt = 4, # mu_opt of the gamma model
temperature_n = 1, # Secondary model for temperature
aw_xmax = 1, aw_xmin = .9, aw_n = 1 # Secondary model for water activity
)
my_start <- list(temperature_xmin = 25, temperature_xopt = 35,
temperature_xmax = 40, aw_xopt = .95)
my_model <- fit_growth(example_dynamic_growth,
sec_models,
my_start, known_pars,
environment = "dynamic",
env_conditions = example_env_conditions
)
## -----------------------------------------------------------------------------
plot(my_model)
## -----------------------------------------------------------------------------
plot(my_model,
line_col = "red",
line_size = 1,
line_type = "dashed",
label_y1 = "Population size (log-millions)",
label_x = "Time (years)",
point_size = 3,
point_shape = 1,
point_col = "darkgrey")
## -----------------------------------------------------------------------------
plot(my_model,
line_col = "red",
line_size = 1,
line_type = "dashed",
label_y1 = "Population size (log-millions)",
label_x = "Time (years)",
point_size = 3,
point_shape = 1,
point_col = "darkgrey") +
theme_gray() +
theme(axis.title = element_text(colour = "green", size = 14))
## -----------------------------------------------------------------------------
plot(my_model) +
coord_cartesian(xlim = c(5, 10), ylim = c(0, 4)) # changing the axis limits
## -----------------------------------------------------------------------------
p1 <- plot(my_model, add_factor = "temperature")
p2 <- plot(my_model, add_factor = "aw")
plot_grid(p1, p2, labels = "AUTO")
## -----------------------------------------------------------------------------
# We save the plot as p1, notice that it does not get drawn now
p1 <- plot(my_model, line_col = "red")
# We save P1 as .pdf, as a 20x 20 cm square
# ggsave("static_prediction.pdf", p1, width = 20, height = 20, units = "cm")
## -----------------------------------------------------------------------------
my_model$best_prediction
## -----------------------------------------------------------------------------
head(my_model$best_prediction$simulation)
## -----------------------------------------------------------------------------
ggplot(my_model$best_prediction$simulation) +
geom_line(aes(x = time, y = Q)) +
scale_y_log10()
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