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longer_term_workflow.R
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library(orderly)
use_draft <- "newer"
## weeks <- seq(
## from = as.Date("2020-10-04"),
## to = as.Date("2020-10-25"),
## by = "7 days"
## )
## weeks <- seq(
## from = as.Date("2020-03-29"),
## to = as.Date("2020-10-25"),
## by = "7 days"
## )
weeks <- seq(
from = as.Date("2020-03-29"), to = as.Date("2020-11-29"),
by = "7 days"
)
weeks <- as.character(weeks)
use_si <- "si_2"
for (week in weeks) {
message("################ ", week, "#############################")
week_ending <- as.Date(week)
parameter <- list(week_ending = week, use_si = use_si)
source("orderly-helper-scripts/dependencies_weights_combined_rt.R")
a <- orderly::orderly_run(
"produce_weights_combined_rt", parameters = parameter, use_draft = use_draft
)
##orderly::orderly_commit(a)
}
for (week in weeks) {
message("################ ", week, "#############################")
week_ending <- as.Date(week)
parameter <- list(week_ending = week, use_si = use_si)
source("orderly-helper-scripts/dependencies_combined_rt.R")
m1 <- orderly::orderly_run(
"produce_combined_rt", parameters = parameter, use_draft = use_draft
)
}
for (week in weeks) {
message("################ ", week, "#############################")
week_ending <- as.Date(week)
parameter <- list(week_ending = week, use_si = use_si)
m2 <- orderly_run(
"produce_longer_forecasts", parameters = parameter,
use_draft = use_draft
)
}
for (week in weeks) {
message("################ ", week, "#############################")
week_ending <- as.Date(week)
parameter <- list(week_ending = week, use_si = use_si)
m2 <- orderly_run(
"produce_longer_forecasts_no_ps", parameters = parameter,
use_draft = use_draft
)
}
for (week in weeks) {
message("################ ", week, "#############################")
week_ending <- as.Date(week)
parameter <- list(week_ending = week, window = 1, latest_week = "2021-01-03")
orderly::orderly_run(
"produce_longer_forecasts_metrics", parameters = parameter, use_draft = use_draft
)
}
for (week in weeks) {
message("################ ", week, "#############################")
parameter <- list(week_ending = week, use_si = use_si)
a <- orderly_run(
"assign_epidemic_phase", parameters = parameter, use_draft = use_draft
)
##orderly::orderly_commit(a)
}
orderly_run("collate_epidemic_phase", use_draft = use_draft)
## Collation
week_starting <- as.Date(head(weeks, 1)[[1]])
week_ending <- as.Date(tail(weeks, 1)[[1]])
source(
"orderly-helper-scripts/dependencies_collate_combined_rt.R"
)
orderly::orderly_run("collate_combined_rt", use_draft = "newer")
source(
"orderly-helper-scripts/dependencies_collate_longer_forecasts.R"
)
orderly::orderly_run("collate_longer_forecasts", use_draft = "newer")
orderly::orderly_run(
"produce_longer_forecasts_viz", use_draft = "newer"
)
source("orderly-helper-scripts/dependencies_collate_longer_forecasts_perf.R")
orderly::orderly_run(
"collate_longer_forecasts_metrics", use_draft = "newer"
)
orderly::orderly_run(
"produce_longer_forecasts_perf_viz", use_draft = "newer"
)