Created
April 25, 2022 15:54
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library("readr") | |
library("dplyr") | |
library("lubridate") | |
library("here") | |
library("tidyr") | |
regional_estimates <- | |
read_csv(paste0("https://raw.githubusercontent.com/epiforecasts/inc2prev/", | |
"master/outputs/estimates_regional.csv")) | |
national_estimates <- | |
read_csv(paste0("https://raw.githubusercontent.com/epiforecasts/inc2prev/", | |
"master/outputs/estimates_national.csv")) | |
estimates <- national_estimates %>% | |
bind_rows(regional_estimates) %>% | |
filter(!is.na(date)) %>% | |
filter(date >= max(date) - weeks(12), | |
level %in% c("national", "regional")) %>% | |
mutate(ValueType = case_when( | |
name == "infections" ~ "incidence", | |
name == "est_prev" ~ "prevalence", | |
name == "r" ~ "growth_rate", | |
name == "R" ~ "R")) %>% | |
filter(!is.na(ValueType)) %>% | |
rename(q05 = q5) %>% ## for sorting | |
select(-name) %>% | |
filter(ValueType %in% c("R", "growth_rate", "incidence", "prevalence")) %>% | |
mutate(Group = "LSHTM", | |
`Creation Day` = day(today()), | |
`Creation Month` = month(today()), | |
`Creation Year` = year(today()), | |
`Day of Value` = day(date), | |
`Month of Value` = month(date), | |
`Year of Value` = year(date)) %>% | |
pivot_longer(matches("^q[0-9]")) %>% | |
arrange(name) %>% | |
mutate(name = paste("Quantile", as.integer(sub("^q", "", name)) / 100)) %>% | |
pivot_wider() %>% | |
mutate(Value = `Quantile 0.5`, | |
Model = "EpiNow ONS Positivity", | |
Scenario = "Nowcast", | |
ModelType = "Survey", | |
Version = "0.1") %>% | |
select(Group, `Creation Day`, `Creation Month`, `Creation Year`, `Day of Value`, | |
`Month of Value`, `Year of Value`, Geography = variable, ValueType, Model, | |
Scenario, ModelType, Version, starts_with("Quantile ")) | |
file_name <- paste(today(), "time-series-ons-cis-lshtm.csv", sep = "-") | |
write_csv(estimates, here::here("format-rt", "data", "cis", file_name)) |
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