# run code
# load required packages
library(ggplot2)
library(tidyr)
library(reshape2)
library(cowplot)
library(stringr)
library(rdist)
library(dplyr)
# load morevac package
# setwd("C:/Users/kainslie/Documents/GitHub/morevac")
setwd("~/Documents/morevac")
devtools::load_all()
# run multi-annual model
out <- multiannual()
# outputs
# plot attack rates
p1 <- plot_attack_rates(dat = out$attack_rate)
# plot lifetime infections
inf_dat <- out$history[,,1]
lifetime_inf <- get_lifetime_inf(inf_history = inf_dat, ages = 1:80, maxage = 80)
# plot drift
mydat <- out$drift
#mydat$Cum_Drift <- cumsum(mydat$Drift)
mydat_thinned <- mydat[which(mydat$Vac_Update==1),]
p_drift <- ggplot(data = mydat, aes(x=Year, y=Drift)) +
geom_line() +
geom_point(data=mydat_thinned,aes(x=Year,y=Drift),colour = 'red')
p_drift
# zoom in on vaccinated years
mydat_vac <- mydat[181:200,]
p_vac <- ggplot(data = mydat_vac, aes(x=Year, y=Drift)) +
geom_line() +
geom_point(data=mydat_thinned,aes(x=Year,y=Drift),colour = 'red')
p_vac
# plot simulated data
setwd("/Volumes/kainslie/morevac_sims/data")
yearRange = 2000:2019
ageRange = 0:19
tags1 <- c("vs0vc50r09v1_w_drift","vs1vc50r09v1_w_drift","vs2vc50r09v1_w_drift") # filename tags
sim_out1 <- read_in_sim_data(tags1) # read in sim results files
dat1 <- process_sim_output(sim_out1, year_range = yearRange, age_range = ageRange) # process sim data
pa1 <- plot_attack_rates(dat = dat1[[1]], by_vac = TRUE, c_bands = TRUE) # plot attack rates
pl1 <- plot_lifetime_infections(dat = dat1[[2]], by_vac = TRUE, x=0.5) # plot lifetime infections
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