In reichlab/covidEnsembles: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)

library(tidyverse)
library(plotly)

#function to read in all csv files with weights 
read_plus <- function(flnm) {
    read_csv(flnm) %>% 
        mutate(filename = flnm)
}

#read in files and add column with filenames 
library(tidyselect)
all_rows <-
    c(list.files("../../../../covid19-forecast-hub/trained_ensemble-metadata/", pattern = "*.csv", 
           full.names = T),
    list.files("forecasts/trained_ensemble-metadata/", pattern = "*.csv", 
           full.names = T)) %>% 
    discard(grepl("thetas.csv",.)) %>% 
    map_df(~read_plus(.)) 

#add columns for targets, dates, and rename locations
df_locations <- all_rows %>% 
  filter(locations %in% c("01", "US")) %>%
  mutate(target = case_when(
    grepl( "cum_death", filename) ~ "cum death",
    grepl("inc_death", filename) ~ "inc death",
    grepl("inc_case",filename) ~ "inc case",
    grepl("inc_hosp",filename) ~ "inc hosp")) %>%
  mutate(date = as.Date(str_extract(filename, "[0-9]{4}-[0-9]{2}-[0-9]{2}"), format="%Y-%m-%d"),
         locations = fct_recode(locations, "State" = "01")) 

#convert dataframe to long format
df_long <- df_locations %>%
  select(-filename) %>%
  pivot_longer(!c(locations, target, date), names_to = "Model", values_to = "Weight") %>% 
  filter(!is.na(Weight)) %>% 
  distinct()

plotly_barplot <- function(target_var, loc_var, title_var) {
  df_long %>% 
  filter(target == target_var) %>%
  filter(locations == loc_var) %>%
  arrange(date) %>%
  plot_ly(
    x = ~date, 
    y = ~Weight, 
    color= ~Model,
    type = 'bar',
           hoverinfo = 'text',
        text = ~paste('</br> Location: ', locations,
                      '</br> Model: ', Model,
                      '</br> Weight: ', round(Weight,4))) %>%
  layout(
    title = title_var,
    xaxis = list(
        type = 'date',
        tickformat = "%d %B %Y"),
    showLegend = FALSE)
}

hosp_state <- plotly_barplot(target_var = "inc hosp",
                            loc_var = "State",
                            title_var = "Incident Hospitalizations") 

hosp_US <- plotly_barplot(target_var = "inc hosp",
                            loc_var = "US",
                            title_var = "Incident Hospitalizations") 

subplot(hosp_state, hosp_US, shareY = T) %>% layout(barmode = 'stack') %>% layout(annotations = list(
 list(x = 0.2 , y = 1.0, text = "State", showarrow = F, xref='paper', yref='paper'),
  list(x = 0.8 , y = 1.0, text = "US", showarrow = F, xref='paper', yref='paper'))
)

case_state <- plotly_barplot(target_var = "inc case",
                            loc_var = "State",
                            title_var = "Incident Cases") 

case_US <- plotly_barplot(target_var = "inc case",
                            loc_var = "US",
                            title_var = "Incident Cases") 

subplot(case_state, case_US, shareY = T) %>% layout(barmode = 'stack') %>% layout(annotations = list(
 list(x = 0.2 , y = 1.0, text = "State", showarrow = F, xref='paper', yref='paper'),
  list(x = 0.8 , y = 1.0, text = "US", showarrow = F, xref='paper', yref='paper')))

inc_state <- plotly_barplot(target_var = "inc death",
                            loc_var = "State",
                            title_var = "Incident Deaths") 

inc_US <- plotly_barplot(target_var = "inc death",
                            loc_var = "US",
                            title_var = "Incident Deaths") 

subplot(inc_state, inc_US, shareY = T) %>% layout(barmode = 'stack') %>% layout(barmode = 'stack') %>% layout(annotations = list(list(x = 0.2 , y = 1.0, text = "State", showarrow = F, xref='paper', yref='paper'),
  list(x = 0.8 , y = 1.0, text = "US", showarrow = F, xref='paper', yref='paper')))

cum_state <- plotly_barplot(target_var = "cum death",
                            loc_var = "State",
                            title_var = "Cumulative Deaths") 

cum_US <- plotly_barplot(target_var = "cum death",
                            loc_var = "US",
                            title_var = "Cumulative Deaths") 

subplot(cum_state, cum_US, shareY = T) %>% layout(barmode = 'stack') %>% layout(annotations = list(
 list(x = 0.2 , y = 1.0, text = "State", showarrow = F, xref='paper', yref='paper'),
  list(x = 0.8 , y = 1.0, text = "US", showarrow = F, xref='paper', yref='paper')))