cal_cat_data_routine.Rmd

---
title: "CalCAT Automation"
author: "Modeling Team"
date: "4/30/2020"
output: html_document
---

```{r setup, include=FALSE}

# Copyright 2020, State of California, Department of Public Health

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knitr::opts_chunk$set(echo = TRUE)

library(readr)
library(stringr)
library(DBI)
library(odbc)
library(pool)
library(dplyr)
library(tidyr)
library(forcats)
library(lubridate)
library(data.table)
library(jsonlite)
library(knitr)
library(rmarkdown)
library(kableExtra)
library(googlesheets4)
library(RSocrata)
library(forecast)

sapply(list.files("R", full.names = T), source)

###############################################################
############         PARAMTERS TO CHANGE        ###############
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state_name <- "California"

counties <- get_counties()
state_abbrv <- get_state_abbrv(State = state_name)
fipslist <- make_fips_list()
rand_state <- get_rand_state_number(State = state_name)
state_fips <- get_state_fips(type = "integer")
state_fips_char <- get_state_fips(type = "character")

data_path <- paste0("data/", state_abbrv,"/")
dir.create(data_path)
dir.create(paste0(data_path, "forecasts/"))
dir.create(paste0(data_path, "nowcasts/"))

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```

## Nowcast/Forecast Data ####
```{r include = FALSE}
### Pull COVID-19 actuals ###
covid_actuals <- grab_hhs_data(state_abbrv)

fwrite(covid_actuals, paste0(data_path, "covid_actuals.csv"))
```

```{r}
covid_admits_arima <- generate_admits_arima(covid_actuals, state_name)

saveRDS(covid_admits_arima, paste0(data_path, "forecasts/covid_admits_arima.rds"))
```

```{r}
covid_admits_damped_holts <- generate_admits_damped_holts(covid_actuals, state_name)

saveRDS(covid_admits_damped_holts, paste0(data_path, "forecasts/covid_admits_damped_holts.rds"))
```

```{r}
covid_admits_holts <- generate_admits_holts(covid_actuals, state_name)

saveRDS(covid_admits_holts, paste0(data_path, "forecasts/covid_admits_holts.rds"))
```

```{r}
covid_admits_NNETAR <- generate_admits_NNETAR(covid_actuals, state_name)

saveRDS(covid_admits_NNETAR, paste0(data_path, "forecasts/covid_admits_NNETAR.rds"))
```

```{r JRC}

deconvolved_dat <- deconvolve_hosp_to_onset(covid_actuals)
jrc <- generate_jrc(deconvolved_dat, state_name)
    
saveRDS(jrc, file.path(data_path, "nowcasts/jrc.rds"))
```

```{r Cislaghi}
#deconvolved_dat <- deconvolve_hosp_to_onset(covid_actuals)
cislaghi <- generate_cislaghi(deconvolved_dat, state_name)
    
saveRDS(cislaghi, file.path(data_path, "nowcasts/cislaghi.rds"))
```

```{r covidestim.org}
covidestim <- grab_covidestim(state_name)

saveRDS(covidestim, file.path(data_path, "nowcasts/covidestim.rds"))

```