Nothing
## ----message=FALSE, warning=FALSE---------------------------------------------
library(epifitter)
library(ggplot2)
library(dplyr)
library(magrittr)
library(cowplot)
## -----------------------------------------------------------------------------
dpcL <- sim_logistic(
N = 100, # duration of the epidemics in days
y0 = 0.01, # disease intensity at time zero
dt = 10, # interval between assessments
r = 0.1, # apparent infection rate
alpha = 0.2, # level of noise
n = 7 # number of replicates
)
## -----------------------------------------------------------------------------
head(dpcL)
## -----------------------------------------------------------------------------
ggplot(
dpcL,
aes(time, y,
group = replicates
)
) +
geom_point(aes(time, random_y), shape = 1) + # plot the replicate values
geom_point(color = "steelblue", size = 2) +
geom_line(color = "steelblue") +
labs(
title = "Simulated 'complete' epidemics of sigmoid shape",
subtitle = "Produced using sim_logistic()"
)+
theme_minimal_hgrid()
## -----------------------------------------------------------------------------
f_lin <- fit_lin(
time = dpcL$time,
y = dpcL$random_y
)
## -----------------------------------------------------------------------------
f_lin
## -----------------------------------------------------------------------------
f_lin$stats_all
## -----------------------------------------------------------------------------
head(f_lin$data)
## -----------------------------------------------------------------------------
plot_lin <- plot_fit(f_lin,
point_size = 2,
line_size = 1
)
# Default plots
plot_lin
## -----------------------------------------------------------------------------
# Customized plots
plot_fit(f_lin,
point_size = 2,
line_size = 1,
models = "Logistic")+
theme_minimal_hgrid(font_size =18) +
scale_x_continuous(limits = c(0,100))+
scale_color_grey()+
theme(legend.position = "none")+
labs(
x = "Time",
y = "Proportion disease "
)
## ----message=FALSE, warning=FALSE---------------------------------------------
f_nlin <- fit_nlin(
time = dpcL$time,
y = dpcL$random_y,
starting_par = list(y0 = 0.01, r = 0.03)
)
f_nlin
## -----------------------------------------------------------------------------
plot_fit(f_nlin) +
theme_minimal_hgrid()#changing plot theme
## -----------------------------------------------------------------------------
dpcL2 = dpcL %>%
mutate(random_y = random_y * 0.8)
## ----message=FALSE, warning=FALSE---------------------------------------------
f_nlin2 <- fit_nlin2(
time = dpcL2$time,
y = dpcL2$random_y,
starting_par = list(y0 = 0.01, r = 0.2, K = 0.6)
)
f_nlin2
plot_fit(f_nlin2)
## -----------------------------------------------------------------------------
epi1 <- sim_gompertz(N = 60, y0 = 0.001, dt = 5, r = 0.1, alpha = 0.4, n = 4)
epi2 <- sim_gompertz(N = 60, y0 = 0.001, dt = 5, r = 0.12, alpha = 0.4, n = 4)
epi3 <- sim_gompertz(N = 60, y0 = 0.003, dt = 5, r = 0.14, alpha = 0.4, n = 4)
multi_epidemic <- bind_rows(epi1,
epi2,
epi3,
.id = "DPC"
)
head(multi_epidemic)
## -----------------------------------------------------------------------------
p_multi <- ggplot(multi_epidemic,
aes(time, y, shape = DPC, group = DPC))+
geom_point(size =2)+
geom_line()+
theme_minimal_grid(font_size =18) +
labs(
x = "Time",
y = "Proportion disease "
)
p_multi
## ----fig.height=10, fig.width=6-----------------------------------------------
p_multi +
facet_wrap(~ DPC, ncol = 1)
## -----------------------------------------------------------------------------
multi_fit <- fit_multi(
time_col = "time",
intensity_col = "random_y",
data = multi_epidemic,
strata_cols = "DPC"
)
## -----------------------------------------------------------------------------
head(multi_fit$Parameters)
## -----------------------------------------------------------------------------
head(multi_fit$Data)
## -----------------------------------------------------------------------------
multi_fit2 <- fit_multi(
time_col = "time",
intensity_col = "random_y",
data = multi_epidemic,
strata_cols = "DPC",
nlin = TRUE)
head(multi_fit2$Parameters)
## -----------------------------------------------------------------------------
multi_fit_K <- fit_multi(
time_col = "time",
intensity_col = "random_y",
data = multi_epidemic,
strata_cols = "DPC",
nlin = T,
estimate_K = T
)
## -----------------------------------------------------------------------------
head(multi_fit_K$Parameters)
## -----------------------------------------------------------------------------
multi_fit$Data %>%
ggplot(aes(time, predicted, color = DPC)) +
geom_point(aes(time, y), color = "gray") +
geom_line(size = 1) +
facet_grid(DPC ~ model, scales = "free_y") +
theme_minimal_hgrid()+
coord_cartesian(ylim = c(0, 1))
## -----------------------------------------------------------------------------
multi_fit$Data %>%
filter(model == "Gompertz") %>%
ggplot(aes(time, predicted, color = DPC)) +
geom_point(aes(time, y),
color = "gray",
size = 2
) +
geom_line(size = 1.2) +
theme_minimal_hgrid() +
labs(
x = "Time",
y = "Disease Intensity"
)
## -----------------------------------------------------------------------------
multi_fit$Parameters %>%
filter(model == "Gompertz") %>%
ggplot(aes(DPC, r)) +
geom_point(size = 3) +
geom_errorbar(aes(ymin = r_ci_lwr, ymax = r_ci_upr),
width = 0,
size = 1
) +
labs(
x = "Time",
y = "Apparent infection rate"
) +
theme_minimal_hgrid()
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