Nothing
## ----message=FALSE, warning=FALSE---------------------------------------------
library(epifitter)
library(magrittr)
library(ggplot2)
library(cowplot)
## -----------------------------------------------------------------------------
exp_model <- sim_exponential(
N = 100, # total time units
y0 = 0.01, # initial inoculum
dt = 10, # interval between assessments in time units
r = 0.045, # apparent infection rate
alpha = 0.2,# level of noise
n = 7 # number of replicates
)
head(exp_model)
## -----------------------------------------------------------------------------
exp_plot = exp_model %>%
ggplot(aes(time, y)) +
geom_jitter(aes(time, random_y), size = 3,color = "gray", width = .1) +
geom_line(size = 1) +
theme_minimal_hgrid() +
ylim(0,1)+
labs(
title = "Exponential",
y = "Disease intensity",
x = "Time"
)
exp_plot
## -----------------------------------------------------------------------------
mono_model <- sim_monomolecular(
N = 100,
y0 = 0.01,
dt = 5,
r = 0.05,
alpha = 0.2,
n = 7
)
head(mono_model)
## -----------------------------------------------------------------------------
mono_plot = mono_model %>%
ggplot(aes(time, y)) +
geom_jitter(aes(time, random_y), size = 3, color = "gray", width = .1) +
geom_line(size = 1) +
theme_minimal_hgrid() +
labs(
title = "Monomolecular",
y = "Disease intensity",
x = "Time"
)
mono_plot
## -----------------------------------------------------------------------------
logist_model <- sim_logistic(
N = 100,
y0 = 0.01,
dt = 5,
r = 0.1,
alpha = 0.2,
n = 7
)
head(logist_model)
## -----------------------------------------------------------------------------
logist_plot = logist_model %>%
ggplot(aes(time, y)) +
geom_jitter(aes(time, random_y), size = 3,color = "gray", width = .1) +
geom_line(size = 1) +
theme_minimal_hgrid() +
labs(
title = "Logistic",
y = "Disease intensity",
x = "Time"
)
logist_plot
## -----------------------------------------------------------------------------
gomp_model <- sim_gompertz(
N = 100,
y0 = 0.01,
dt = 5,
r = 0.07,
alpha = 0.2,
n = 7
)
head(gomp_model)
## -----------------------------------------------------------------------------
gomp_plot = gomp_model %>%
ggplot(aes(time, y)) +
geom_jitter(aes(time, random_y), size = 3,color = "gray", width = .1) +
geom_line(size = 1) +
theme_minimal_hgrid() +
labs(
title = "Gompertz",
y = "Disease intensity",
x = "Time"
)
gomp_plot
## ----fig.height=6, fig.width=8------------------------------------------------
plot_grid(exp_plot,
mono_plot,
logist_plot,
gomp_plot)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.