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Change config for Canada #15

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Merged
dajmcdon merged 4 commits into from
Apr 19, 2022
Merged

Change config for Canada #15

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63317fa
change some configurations for Canada
lzlzlizi Apr 19, 2022
2b13288
Merge branch 'cmu-delphi:main' into main
lzlzlizi Apr 19, 2022
23962a9
remove local installation
lzlzlizi Apr 19, 2022
0662765
merge
lzlzlizi Apr 19, 2022
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36 changes: 24 additions & 12 deletions vignettes/simple-forecasts.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -177,36 +177,48 @@ can <- readRDS(
) %>%
group_by(version, geo_value) %>%
arrange(time_value) %>%
mutate(cr_7dav = RcppRoll::roll_meanr(case_rate, n = 7L))
mutate(cr_7dav = RcppRoll::roll_meanr(case_rate, n = 7L)) #%>%
#filter(geo_value %in% c('Alberta', "BC"))
can <- as_epi_archive(can)
can_latest <- epix_as_of(can, max_version = max(can$DT$version))

can_k_week_ahead <- function(ahead = 7) {
can %>%
epix_slide(fc = arx_forecaster(
y = cr_7dav, key_vars = geo_value, time_value = time_value,
args = arx_args_list(ahead = ahead)),
n = 120, ref_time_values = fc_time_values, group_by = geo_value) %>%
mutate(target_date = time_value + ahead)
can_k_week_ahead <- function(x, ahead = 7, as_of = TRUE) {
if(as_of){
can %>%
epix_slide(fc = arx_forecaster(
y = cr_7dav, key_vars = geo_value, time_value = time_value,
args = arx_args_list(intercept = FALSE,ahead = ahead)),
n = 120, ref_time_values = fc_time_values) %>%
mutate(target_date = time_value + ahead, geo_value = fc_key_vars, as_of = as_of)
}
else{
can_latest %>%
epi_slide(fc = arx_forecaster(
y = cr_7dav, key_vars = geo_value, time_value = time_value,
args = arx_args_list(intercept = FALSE,ahead = ahead)),
n = 120, ref_time_values = fc_time_values) %>%
mutate(target_date = time_value + ahead, geo_value = fc_key_vars, as_of = as_of)
}
}

can_fc <- purrr:::map_dfr(c(7,14,21,28), ~ can_k_week_ahead(.x))
can_fc <- bind_rows(purrr:::map_dfr(c(7,14,21,28), ~ can_k_week_ahead(can, ahead = .x, as_of = TRUE)),
purrr:::map_dfr(c(7,14,21,28), ~ can_k_week_ahead(can_latest, ahead = .x, as_of = FALSE)))
```

The figure below shows the results for all of the provinces. Note that we are showing the 7-day averages rather than the reported case numbers due to highly variable provincial reporting mismatches.

```{r plot-can-fc, message = FALSE, warning = FALSE, fig.width = 9, fig.height = 12}
can_latest <- epix_as_of(can, max_version = max(x$DT$version))
ggplot(can_fc, aes(x = target_date, group = time_value)) +
coord_cartesian(xlim = lubridate::ymd(c("2020-12-01", NA))) +
geom_line(data = can_latest, aes(x = time_value, y = cr_7dav),
inherit.aes = FALSE, color = "gray50") +
geom_ribbon(aes(ymin = fc_q0.05, ymax = fc_q0.95, fill = geo_value), alpha = 0.4) +
geom_line(aes(y = fc_point)) + geom_point(aes(y = fc_point), size = 0.5) +
geom_vline(aes(xintercept = time_value), linetype = 2, alpha = 0.5) +
facet_wrap(~geo_value, scales = "free", ncol = 3) +
facet_wrap(paste('as_of: ', as_of)~geo_value,scales = "free",ncol = 4) +
scale_x_date(minor_breaks = "month", date_labels = "%b %y") +
labs(x = "Date", y = "Reported COVID-19 case rates") +
theme(legend.position = "none")
theme(legend.position = "none")
```

## Goals for `epipredict`
Expand Down