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nowcast-US-cases-simulation_validation.Rmd
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---
title: ""
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
html_document:
df_print: paged
---
```{r setup, include=FALSE}
library(tidyverse)
library(tibbletime)
library(padr)
library(tvReg)
library(forecast)
library(here)
source(here::here('R/package.R'))
source(here::here('R/deconcolve.R'))
source(here::here('R/simple_tdar.R'))
source(here::here('R/package_tv.R'))
source(here::here('R/nowcast.R'))
```
<!-- Get simultations for US states -->
```{r data, include=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim <- read_csv(here::here("data/nowcast-validation-1.csv")) %>%
rename(Date = X1) %>%
mutate(Date = as.Date("2019-11-30") + Date) %>%
replace(., is.na(.), 0) %>%
tibbletime::as_tbl_time(index=Date)
US.sim2 <- read_csv(here::here("data/nowcast-validation-2.csv")) %>%
rename(Date = X1) %>%
mutate(Date = as.Date("2019-11-30") + Date) %>%
replace(., is.na(.), 0) %>%
tibbletime::as_tbl_time(index=Date)
US.sim3 <- read_csv(here::here("data/nowcast-validation-3.csv")) %>%
rename(Date = X1) %>%
mutate(Date = as.Date("2019-11-30") + Date) %>%
replace(., is.na(.), 0) %>%
tibbletime::as_tbl_time(index=Date)
US.sim4 <- read_csv(here::here("data/nowcast-validation-4.csv")) %>%
rename(Date = X1) %>%
mutate(Date = as.Date("2019-11-30") + Date) %>%
replace(., is.na(.), 0) %>%
tibbletime::as_tbl_time(index=Date)
US.sim5 <- read_csv(here::here("data/nowcast-validation-5.csv")) %>%
rename(Date = X1) %>%
mutate(Date = as.Date("2019-11-30") + Date) %>%
replace(., is.na(.), 0) %>%
tibbletime::as_tbl_time(index=Date)
US.sim5b <- read_csv(here::here("data/nowcast-validation-Scenario-5.csv")) %>%
rename(Date = X1) %>%
mutate(Date = as.Date("2019-11-30") + Date) %>%
replace(., is.na(.), 0) %>%
tibbletime::as_tbl_time(index=Date)
US.sim6 <- read_csv(here::here("data/nowcast-validation-Scenario-6.csv")) %>%
rename(Date = X1) %>%
mutate(Date = as.Date("2019-11-30") + Date) %>%
replace(., is.na(.), 0) %>%
tibbletime::as_tbl_time(index=Date)
US.sim7 <- read_csv(here::here("data/nowcast-validation-Scenario-7.csv")) %>%
rename(Date = X1) %>%
mutate(Date = as.Date("2019-11-30") + Date) %>%
replace(., is.na(.), 0) %>%
tibbletime::as_tbl_time(index=Date)
```
# Simulation 1
```{r, echo = TRUE}
US.params <- list(admin = "US", # state or country
q = 1, # Detection probability
a = 0.346, # Proportion of cases that are asymptomatic
c = 1, # Transmissability of undetectable cases
effective.infectious.period = list(dist="exponential", mean=2.67),
infectious.period = list(dist="exponential", mean=7),
incubation.period = list(dist="gamma", mean=7.67, shape=4.1775942)
)
```
```{r, echo=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim.nowcast <- US.sim %>% select(Date, cases = case.notifications) %>%
mutate(sim.unobserved = US.sim$unobserved) %>%
tbl_time(index = Date) %>% nowcast_from_case_reports(US.params)
maxy <- max(US.sim.nowcast$cases, US.sim.nowcast$unobserved, US.sim.nowcast$nowcast.mean, US.sim.nowcast$nowcast.upper95)
plot(x=US.sim.nowcast$Date, y=US.sim.nowcast$cases, type = "l", xlim=range(US.sim.nowcast$Date),ylim=c(0,maxy))
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$sim.unobserved,col="blue",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.mean,col="purple",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.lower95,col="purple",type="l", lty = "dotted")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.upper95,col="purple",type="l", lty = "dotted")
title(main = "simulation 1")
plot(x = US.sim.nowcast$nowcast.mean, y = US.sim.nowcast$sim.unobserved, type = "l", asp="1")
lines(x = US.sim.nowcast$nowcast.upper95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
lines(x = US.sim.nowcast$nowcast.lower95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
abline(0, 1)
title(main = "simulation 1")
```
# Simulation 2
```{r, echo = TRUE}
US.params <- list(admin = "US", # state or country
q = 1, # Detection probability
a = 0.346, # Proportion of cases that are asymptomatic
c = 1, # Transmissability of undetectable cases
effective.infectious.period = list(dist="exponential", mean=2.67),
infectious.period = list(dist="exponential", mean=7),
incubation.period = list(dist="gamma", mean=7.67, shape=4.1775942)
)
```
```{r, echo=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim.nowcast <- US.sim2 %>% select(Date, cases = case.notifications) %>%
mutate(sim.unobserved = US.sim2$unobserved) %>%
tbl_time(index = Date) %>% nowcast_from_case_reports(US.params)
maxy <- max(US.sim.nowcast$cases, US.sim.nowcast$unobserved, US.sim.nowcast$nowcast.mean, US.sim.nowcast$nowcast.upper95)
plot(x=US.sim.nowcast$Date, y=US.sim.nowcast$cases, type = "l", xlim=range(US.sim.nowcast$Date),ylim=c(0,maxy))
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$sim.unobserved,col="blue",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.mean,col="purple",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.lower95,col="purple",type="l", lty = "dotted")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.upper95,col="purple",type="l", lty = "dotted")
title(main = "simulation 2")
plot(x = US.sim.nowcast$nowcast.mean, y = US.sim.nowcast$sim.unobserved, type = "l", asp="1")
lines(x = US.sim.nowcast$nowcast.upper95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
lines(x = US.sim.nowcast$nowcast.lower95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
abline(0, 1)
title(main = "simulation 2")
```
# Simulation 3
```{r, echo = TRUE}
US.params <- list(admin = "US", # state or country
q = 1, # Detection probability
a = 0.346, # Proportion of cases that are asymptomatic
c = 1, # Transmissability of undetectable cases
effective.infectious.period = list(dist="exponential", mean=2.67),
infectious.period = list(dist="exponential", mean=7),
incubation.period = list(dist="gamma", mean=7.67, shape=4.1775942)
)
```
```{r, echo=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim.nowcast <- US.sim3 %>% select(Date, cases = case.notifications) %>%
mutate(sim.unobserved = US.sim3$unobserved) %>%
tbl_time(index = Date) %>% nowcast_from_case_reports(US.params)
maxy <- max(US.sim.nowcast$cases, US.sim.nowcast$unobserved, US.sim.nowcast$nowcast.mean, US.sim.nowcast$nowcast.upper95)
plot(x=US.sim.nowcast$Date, y=US.sim.nowcast$cases, type = "l", xlim=range(US.sim.nowcast$Date),ylim=c(0,maxy))
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$sim.unobserved,col="blue",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.mean,col="purple",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.lower95,col="purple",type="l", lty = "dotted")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.upper95,col="purple",type="l", lty = "dotted")
title(main = "simulation 3")
plot(x = US.sim.nowcast$nowcast.mean, y = US.sim.nowcast$sim.unobserved, type = "l", asp="1")
lines(x = US.sim.nowcast$nowcast.upper95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
lines(x = US.sim.nowcast$nowcast.lower95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
abline(0, 1)
title(main = "simulation 3")
```
# Simulation 4
```{r, echo = TRUE}
US.params <- list(admin = "US", # state or country
q = 1, # Detection probability
a = 0, # Proportion of cases that are asymptomatic
c = 1, # Transmissability of undetectable cases
effective.infectious.period = list(dist="exponential", mean=2.67),
infectious.period = list(dist="exponential", mean=7),
incubation.period = list(dist="gamma", mean=7.67, shape=4.1775942)
)
```
```{r, echo=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim.nowcast <- US.sim4 %>% select(Date, cases = case.notifications) %>%
mutate(sim.unobserved = US.sim4$unobserved) %>%
tbl_time(index = Date) %>% nowcast_from_case_reports(US.params)
maxy <- max(US.sim.nowcast$cases, US.sim.nowcast$unobserved, US.sim.nowcast$nowcast.mean, US.sim.nowcast$nowcast.upper95)
plot(x=US.sim.nowcast$Date, y=US.sim.nowcast$cases, type = "l", xlim=range(US.sim.nowcast$Date),ylim=c(0,maxy))
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$sim.unobserved,col="blue",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.mean,col="purple",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.lower95,col="purple",type="l", lty = "dotted")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.upper95,col="purple",type="l", lty = "dotted")
title(main = "simulation 4")
plot(x = US.sim.nowcast$nowcast.mean, y = US.sim.nowcast$sim.unobserved, type = "l", asp="1")
lines(x = US.sim.nowcast$nowcast.upper95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
lines(x = US.sim.nowcast$nowcast.lower95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
abline(0, 1)
title(main = "simulation 4")
```
# Simulation 5
```{r, echo = TRUE}
US.params <- list(admin = "US", # state or country
q = 1, # Detection probability
a = 0, # Proportion of cases that are asymptomatic
c = 1, # Transmissability of undetectable cases
effective.infectious.period = list(dist="exponential", mean=2.67),
infectious.period = list(dist="exponential", mean=7),
incubation.period = list(dist="gamma", mean=7.67, shape=4.1775942)
)
```
```{r, echo=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim.nowcast <- US.sim5 %>% select(Date, cases = case.notifications) %>%
mutate(sim.unobserved = US.sim5$unobserved) %>%
tbl_time(index = Date) %>% nowcast_from_case_reports(US.params)
maxy <- max(US.sim.nowcast$cases, US.sim.nowcast$unobserved, US.sim.nowcast$nowcast.mean, US.sim.nowcast$nowcast.upper95)
plot(x=US.sim.nowcast$Date, y=US.sim.nowcast$cases, type = "l", xlim=range(US.sim.nowcast$Date),ylim=c(0,maxy))
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$sim.unobserved,col="blue",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.mean,col="purple",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.lower95,col="purple",type="l", lty = "dotted")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.upper95,col="purple",type="l", lty = "dotted")
title(main = "simulation 5")
plot(x = US.sim.nowcast$nowcast.mean, y = US.sim.nowcast$sim.unobserved, type = "l", asp="1")
lines(x = US.sim.nowcast$nowcast.upper95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
lines(x = US.sim.nowcast$nowcast.lower95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
abline(0, 1)
title(main = "simulation 5")
```
# Simulation 5b
```{r, echo = TRUE}
US.params <- list(admin = "US", # state or country
q = 1, # Detection probability
a = 0, # Proportion of cases that are asymptomatic
c = 1, # Transmissability of undetectable cases
effective.infectious.period = list(dist="exponential", mean=2.67),
infectious.period = list(dist="exponential", mean=7),
incubation.period = list(dist="gamma", mean=7.67, shape=4.1775942)
)
```
```{r, echo=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim.nowcast <- US.sim5b %>% select(Date, cases = case.notifications) %>%
mutate(sim.unobserved = US.sim5b$unobserved) %>%
tbl_time(index = Date) %>% nowcast_from_case_reports(US.params)
maxy <- max(US.sim.nowcast$cases, US.sim.nowcast$unobserved, US.sim.nowcast$nowcast.mean, US.sim.nowcast$nowcast.upper95)
plot(x=US.sim.nowcast$Date, y=US.sim.nowcast$cases, type = "l", xlim=range(US.sim.nowcast$Date),ylim=c(0,maxy))
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$sim.unobserved,col="blue",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.mean,col="purple",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.lower95,col="purple",type="l", lty = "dotted")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.upper95,col="purple",type="l", lty = "dotted")
title(main = "simulation 5b")
plot(x = US.sim.nowcast$nowcast.mean, y = US.sim.nowcast$sim.unobserved, type = "l", asp="1")
lines(x = US.sim.nowcast$nowcast.upper95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
lines(x = US.sim.nowcast$nowcast.lower95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
abline(0, 1)
title(main = "simulation 5b")
```
# Simulation 6
```{r, echo = TRUE}
US.params <- list(admin = "US", # state or country
q = 1, # Detection probability
a = 0, # Proportion of cases that are asymptomatic
c = 1, # Transmissability of undetectable cases
effective.infectious.period = list(dist="exponential", mean=2.67),
infectious.period = list(dist="exponential", mean=7),
incubation.period = list(dist="gamma", mean=7.67, shape=4.1775942)
)
```
```{r, echo=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim.nowcast <- US.sim6 %>% select(Date, cases = case.notifications) %>%
mutate(sim.unobserved = US.sim6$unobserved) %>%
tbl_time(index = Date) %>% nowcast_from_case_reports(US.params)
maxy <- max(US.sim.nowcast$cases, US.sim.nowcast$unobserved, US.sim.nowcast$nowcast.mean, US.sim.nowcast$nowcast.upper95)
plot(x=US.sim.nowcast$Date, y=US.sim.nowcast$cases, type = "l", xlim=range(US.sim.nowcast$Date),ylim=c(0,maxy))
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$sim.unobserved,col="blue",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.mean,col="purple",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.lower95,col="purple",type="l", lty = "dotted")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.upper95,col="purple",type="l", lty = "dotted")
title(main = "simulation 6")
plot(x = US.sim.nowcast$nowcast.mean, y = US.sim.nowcast$sim.unobserved, type = "l", asp="1")
lines(x = US.sim.nowcast$nowcast.upper95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
lines(x = US.sim.nowcast$nowcast.lower95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
abline(0, 1)
title(main = "simulation 6")
```
# simulation 7
```{r, echo = TRUE}
US.params <- list(admin = "US", # state or country
q = 1, # Detection probability
a = 0, # Proportion of cases that are asymptomatic
c = 1, # Transmissability of undetectable cases
effective.infectious.period = list(dist="gamma", mean=4.4, shape=1.9816403),
infectious.period = list(dist="exponential", mean=7),
incubation.period = list(dist="gamma", mean=7.67, shape=4.1775942)
)
```
```{r, echo=FALSE, message = FALSE, warning = FALSE, cache = FALSE}
US.sim.nowcast <- US.sim7 %>% select(Date, cases = case.notifications) %>%
mutate(sim.unobserved = US.sim7$unobserved) %>%
tbl_time(index = Date) %>% nowcast_from_case_reports(US.params)
maxy <- max(US.sim.nowcast$cases, US.sim.nowcast$unobserved, US.sim.nowcast$nowcast.mean, US.sim.nowcast$nowcast.upper95)
plot(x=US.sim.nowcast$Date, y=US.sim.nowcast$cases, type = "l", xlim=range(US.sim.nowcast$Date),ylim=c(0,maxy))
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$sim.unobserved,col="blue",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.mean,col="purple",type="l")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.lower95,col="purple",type="l", lty = "dotted")
lines(x=US.sim.nowcast$Date, y=US.sim.nowcast$nowcast.upper95,col="purple",type="l", lty = "dotted")
title(main = "simulation 7")
plot(x = US.sim.nowcast$nowcast.mean, y = US.sim.nowcast$sim.unobserved, type = "l", asp="1")
lines(x = US.sim.nowcast$nowcast.upper95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
lines(x = US.sim.nowcast$nowcast.lower95, y = US.sim.nowcast$sim.unobserved, type = "l", lty="dotted")
abline(0, 1, lty="dashed")
title(main = "simulation 7")
```