In kmcconeghy/flumodelr: An R Package for Estimating Attributable Influenza Morbidity and Mortality

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
options(tibble.print_min = 4L, tibble.print_max = 4L)
library(flumodelr)
library(lubridate)
library(scales)
library(forecast)

Generalized additive models (GAM)

Influenza data

fludta <- flumodelr::fludta
fludta

GAM

gam_1 <- gam(fludeaths ~ s(week_in_order, bs='ps'), family=nb(), data=test)
summary(gam_1)

plot(gam_1, shade=T)

`flugam` function

Using only off-season as baseline

fit <- fludta %>%
  bind_cols(., flugam(data=fludta, outc=fludeaths, time=week_in_order, season=epi))

#Set up graph labels, line specs
line_names <- c("Deaths From P&I", "Expected", "Baseline")
line_cols <- c("#CC0000", "black", "black")
line_types <- c(1, 1, 2)
names(line_cols) <- line_names
names(line_types) <- line_names

ggplot(fit, aes(x=yrweek_dt)) + 
  geom_line(aes(y=fludeaths, colour=line_names[[1]], 
                linetype=line_names[[1]]), size=0.8) +
  geom_line(aes(y=flu_pred, colour=line_names[[2]], 
                linetype=line_names[[2]]), size=0.8) +
  geom_line(aes(y=flu_base_upr, colour=line_names[[3]], 
                linetype=line_names[[3]]), size=0.8) +
  scale_colour_manual("Line", breaks=line_names, values = line_cols) +
  scale_linetype_manual("Line",  breaks=line_names, values = line_types) +
  scale_x_date(labels = date_format("%Y"), date_breaks="1 year",
               expand=c(0, .9)) + 
  xlab("Year") + 
  ylab("% of Deaths from P&I") + 
  theme_light(base_size=14) +
  theme(legend.text=element_text(size=10), 
        plot.title = element_text(size=14)) +
  labs(title="Figure 1. Pneumonia and Influenza Mortality",
       caption="Generalized additive model - Seasonal only") +
  guides(colour = guide_legend("Line"), linetype = guide_legend("Line"))

Using viral data as baseline

fit <- fludta %>%
  bind_cols(., flugam(data=fludta, outc=fludeaths, 
                      time=week_in_order, viral='prop_flupos'))

#Set up graph labels, line specs
line_names <- c("Deaths From P&I", "Expected", "Baseline")
line_cols <- c("#CC0000", "black", "black")
line_types <- c(1, 1, 2)
names(line_cols) <- line_names
names(line_types) <- line_names

ggplot(fit, aes(x=yrweek_dt)) + 
  geom_line(aes(y=fludeaths, colour=line_names[[1]], 
                linetype=line_names[[1]]), size=0.8) +
  geom_line(aes(y=flu_pred, colour=line_names[[2]], 
                linetype=line_names[[2]]), size=0.8) +
  geom_line(aes(y=flu_base_upr, colour=line_names[[3]], 
                linetype=line_names[[3]]), size=0.8) +
  scale_colour_manual("Line", breaks=line_names, values = line_cols) +
  scale_linetype_manual("Line",  breaks=line_names, values = line_types) +
  scale_x_date(labels = date_format("%Y"), date_breaks="1 year",
               expand=c(0, .9)) + 
  xlab("Year") + 
  ylab("% of Deaths from P&I") + 
  theme_light(base_size=14) +
  theme(legend.text=element_text(size=10), 
        plot.title = element_text(size=14)) +
  labs(title="Figure 2. Pneumonia and Influenza Mortality",
       caption="Generalized additive model - Viral added") +
  guides(colour = guide_legend("Line"), linetype = guide_legend("Line"))