submission/launch.R

In signaturescience/focustools: Forecasting COVID-19 in the United States (FOCUS) tools

## script to run automated app pipeline
## NOTE: if used locally edit submission dir as needed
## using here::here("submission", "SigSci-TS") was not working on app refresh
submission_dir <- "/submission/SigSci-TS"

library(focustools)
library(tidyverse)

## Get national data
national <- inner_join(
  get_cases( source="jhu", granularity="national"),
  get_deaths(source="jhu", granularity="national"),
  by = c("location", "epiyear", "epiweek"))
## Get state data
state <- inner_join(
  get_cases( source="jhu", granularity="state"),
  get_deaths(source="jhu", granularity="state"),
  by = c("location", "epiyear", "epiweek"))
## combine US and state data
usafull <-
  bind_rows(national, state) %>%
  filter(location %in% c("US", stringr::str_pad(1:56, width=2, pad="0"))) %>%
  make_tsibble() %>%
  filter(monday>"2020-03-01")

focus_explorer(.data = usafull,
               submission_dir = submission_dir,
               host = "0.0.0.0",
               port = 3838,
               launch.browser = TRUE)