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jidea-110 New time series #30

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jidea-110 New time series #30

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640d6fa
add new time series
EmmaLRussell Oct 21, 2024
7d7d610
time series metadata
EmmaLRussell Oct 21, 2024
9e01b1d
add metadata
EmmaLRussell Oct 21, 2024
1276b19
unit test
EmmaLRussell Oct 21, 2024
b1442da
fix schema
EmmaLRussell Oct 21, 2024
c8bd90a
test get_incidence calls
EmmaLRussell Oct 21, 2024
5bdcc2d
lint
EmmaLRussell Oct 21, 2024
c66e074
more lint
EmmaLRussell Oct 21, 2024
aa1d4a5
call get_incidence once only
EmmaLRussell Oct 21, 2024
6286cda
update time series names
EmmaLRussell Oct 21, 2024
c601838
update new hosp description
EmmaLRussell Oct 21, 2024
140b7cc
shorten long line
EmmaLRussell Oct 21, 2024
4c793d1
update e2e test
EmmaLRussell Oct 21, 2024
3f5e97b
lint
EmmaLRussell Oct 21, 2024
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12 changes: 12 additions & 0 deletions R/model_run.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,18 @@ model_run <- function(parameters, model_version) {
)
time_series$vaccinated <- vax_time_series$vaccinated

# get incidence time series
incidences <- daedalus::get_incidence(model_results)
incidences <- tidyr::pivot_wider(
incidences, id_cols = "time", names_from = "measure"
)
time_series$new_infected <- incidences$daily_infections
time_series$new_hospitalised <- incidences$daily_hospitalisations
time_series$new_dead <- incidences$daily_deaths

time_series$new_vaccinated <-
daedalus::get_new_vaccinations(model_results)$new_vaccinations

raw_costs <- daedalus::get_costs(model_results)
costs <- get_nested_costs(raw_costs)

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44 changes: 43 additions & 1 deletion inst/json/metadata_0.1.0.json
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Expand Up @@ -107,7 +107,49 @@
"description": "Number of infectious individuals, comprising both symptomatic and asymptomatic infections, including those in need of hospitalisation." },
{ "id": "hospitalised", "label": "Hospital demand", "description": "Infections requiring hospitalisation" },
{ "id": "dead", "label": "Dead", "description": "Total deaths" },
{ "id": "vaccinated", "label": "Vaccinated", "description": "Total number of vaccinations administered" }
{ "id": "vaccinated", "label": "Vaccinated", "description": "Total number of vaccinations administered" },
{ "id": "new_infected", "label": "New infections", "description": "Number of new infections per day" },
{ "id": "new_hospitalised", "label": "New hospitalisations", "description": "Number of new patients in need of hospitalisation per day" },
{ "id": "new_dead", "label": "New deaths", "description": "Number of deaths per day" },
{ "id": "new_vaccinated", "label": "New vaccinations", "description": "Number of vaccinations per day" }
],
"time_series_roles": [
{"id": "total", "label": "Total"},
{"id": "daily", "label": "Daily"}
],
"time_series_groups": [
{
"id": "infections",
"label": "Infections",
"time_series": {
"total": "prevalence",
"daily": "new_infected"
}
},
{
"id": "hospitalisations",
"label": "Hospitalisations",
"time_series": {
"total": "hospitalised",
"daily": "new_hospitalised"
}
},
{
"id": "deaths",
"label": "Deaths",
"time_series": {
"total": "dead",
"daily": "new_dead"
}
},
{
"id": "vaccinations",
"label": "Vaccinations",
"time_series": {
"total": "vaccinated",
"daily": "new_vaccinated"
}
}
]
}
}
19 changes: 19 additions & 0 deletions inst/schema/metadata.json
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Expand Up @@ -93,6 +93,25 @@
"items": {
"$ref": "#/$defs/displayInfo"
}
},
"time_series_roles": {
"type": "array",
"items": {
"$ref": "#/$defs/displayInfo"
}
},
"time_series_groups": {
"type": "array",
"items": {
"type": "object",
"properties": {
"id": { "type": "string" },
"label": { "type": "string" },
"time_series": { "type": "object" }
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@david-mears-2 david-mears-2 Oct 21, 2024 •
edited
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Is there no way to specify that this object's keys must be 'time_series_role's? If not, what good does it do to define the time_series_roles array?

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@EmmaLRussell EmmaLRussell Oct 21, 2024 •
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I don't think so, in the schema. The reason for putting in the time_series_roles array was to include metadata, which the front end might choose to use i.e. label.

},
"additionalProperties": false,
"required": ["id", "label", "time_series"]
}
}
},
"additionalProperties": false,
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5 changes: 5 additions & 0 deletions tests/testthat/test-zzz-e2e.R
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Expand Up @@ -91,6 +91,11 @@ test_that("can run model, get status and results", {
expect_length(results_data$time_series$prevalence, time_series_length)
expect_length(results_data$time_series$hospitalised, time_series_length)
expect_length(results_data$time_series$dead, time_series_length)
expect_length(results_data$time_series$new_infected, time_series_length)
expect_length(results_data$time_series$new_hospitalised,
time_series_length)
expect_length(results_data$time_series$new_dead, time_series_length)
expect_length(results_data$time_series$new_vaccinated, time_series_length)

expect_gt(results_data$gdp, 0)

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32 changes: 31 additions & 1 deletion tests/testthat/test_model_run.R
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Expand Up @@ -14,6 +14,22 @@ test_that("can run model and return results", {

mockery::stub(model_run, "daedalus::get_data", mock_model_data)

mock_incidence_result <- data.frame(
time = c(1, 2, 1, 2, 1, 2),
measure = c("daily_infections", "daily_infections",
"daily_hospitalisations", "daily_hospitalisations",
"daily_deaths", "daily_deaths"),
value = c(100L, 200L, 10L, 20L, 1L, 2L),
stringsAsFactors = FALSE
)
mock_get_incidence <- mockery::mock(mock_incidence_result,
cycle = TRUE)
mockery::stub(model_run, "daedalus::get_incidence", mock_get_incidence)

mock_new_vaccinations_result <- list(new_vaccinations = c(100, 200))
mockery::stub(model_run, "daedalus::get_new_vaccinations",
mock_new_vaccinations_result)

mock_costs_data <- daedalus_mock_costs()
mock_get_costs <- mockery::mock(mock_costs_data)
mockery::stub(model_run, "daedalus::get_costs", mock_get_costs)
Expand All @@ -39,6 +55,11 @@ test_that("can run model and return results", {
)
)

expect_identical(
mockery::mock_args(mock_get_incidence)[[1]],
list(mock_results)
)

expect_named(res, c(
"parameters",
"costs",
Expand All @@ -50,11 +71,20 @@ test_that("can run model and return results", {
expect_named(res$time_series, c("prevalence",
"hospitalised",
"dead",
"vaccinated"))
"vaccinated",
"new_infected",
"new_hospitalised",
"new_dead",
"new_vaccinated"))
expect_identical(res$time_series$prevalence, c(28L, 87L))
expect_identical(res$time_series$hospitalised, c(11L, 31L))
expect_identical(res$time_series$dead, c(15L, 37L))
expect_identical(res$time_series$vaccinated, c(1L, 5L))
expect_identical(res$time_series$new_infected, c(100L, 200L))
expect_identical(res$time_series$new_hospitalised, c(10L, 20L))
expect_identical(res$time_series$new_dead, c(1L, 2L))
expect_identical(res$time_series$new_vaccinated,
mock_new_vaccinations_result$new_vaccinations)
expect_identical(res$parameters, parameters)
expect_nested_mock_costs(res$costs)
expect_identical(res$interventions, list(
Expand Down
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