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Merge pull request #45 from tuxette/testthat
first version of the tests based on examples
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@@ -62,5 +62,6 @@ Suggests: | |
| rmarkdown, | ||
| fable, | ||
| feasts, | ||
| future.apply | ||
| future.apply, | ||
| testthat | ||
| VignetteBuilder: knitr | ||
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| codecov: | ||
| token: 3b555487-3534-4ebf-9985-546286a42ed9 | ||
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| library("testthat") | ||
| library("EpiSoon") | ||
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| test_check("EpiSoon") |
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| ##------------------------------------------------------------ | ||
| context("Test of the function 'compare_models'.... testing outputs") | ||
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| models <- list("AR 3" = function(...) { | ||
| EpiSoon::bsts_model(model = function(ss, y){ | ||
| bsts::AddAr(ss, y = y, lags = 3) | ||
| }, ...)}, | ||
| "Semi-local linear trend" = function(...) { | ||
| EpiSoon::bsts_model(model = function(ss, y){ | ||
| bsts::AddSemilocalLinearTrend(ss, y = y) | ||
| }, ...)} | ||
| ) | ||
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| out <- compare_models(EpiSoon::example_obs_rts, | ||
| EpiSoon::example_obs_cases, | ||
| models, | ||
| horizon = 7, samples = 10, | ||
| serial_interval = EpiSoon::example_serial_interval) | ||
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| test_that("Outputs have proper lenghts and names", { | ||
| expect_length(out, 4) | ||
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| expect_named(out, c("forecast_rts", "rt_scores", "forecast_cases", "case_scores")) | ||
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| # 'return_raw' version | ||
| out_raw <- compare_models(EpiSoon::example_obs_rts, | ||
| EpiSoon::example_obs_cases, | ||
| models, | ||
| horizon = 7, samples = 10, | ||
| serial_interval = EpiSoon::example_serial_interval, | ||
| return_raw = TRUE) | ||
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| expect_length(out_raw, 6) | ||
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| expect_named(out_raw, c("forecast_rts", "rt_scores", "forecast_cases", | ||
| "case_scores", "raw_rt_forecast", "raw_case_forecast")) | ||
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| }) | ||
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| test_that("Outputs return results for all models", { | ||
| expect_identical(names(models), unique(out$forecast_rts$model)) | ||
| expect_equal(sum(is.na(out$forecast_rts)), 0) | ||
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| expect_identical(names(models), unique(out$rt_scores$model)) | ||
| expect_equal(sum(is.na(out$rt_scores)), 0) | ||
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| expect_identical(names(models), unique(out$forecast_cases$model)) | ||
| expect_equal(sum(is.na(out$forecast_cases)), 0) | ||
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| expect_identical(names(models), unique(out$case_scores$model)) | ||
| expect_equal(sum(is.na(out$case_scores)), 0) | ||
| }) |
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| ##------------------------------------------------------------ | ||
| context("Test of the function 'compare_timeseries'.... testing outputs") | ||
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| obs_rts <- EpiSoon::example_obs_rts %>% | ||
| dplyr::mutate(timeseries = "Region 1") %>% | ||
| dplyr::bind_rows(EpiSoon::example_obs_rts %>% | ||
| dplyr::mutate(timeseries = "Region 2")) | ||
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| obs_cases <- EpiSoon::example_obs_cases %>% | ||
| dplyr::mutate(timeseries = "Region 1") %>% | ||
| dplyr::bind_rows(EpiSoon::example_obs_cases %>% | ||
| dplyr::mutate(timeseries = "Region 2")) | ||
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| models <- list("AR 3" = function(...){ | ||
| EpiSoon::bsts_model(model = function(ss, y){ | ||
| bsts::AddAr(ss, y = y, lags = 3) | ||
| }, ...)}, | ||
| "Semi-local linear trend" = function(...) { | ||
| EpiSoon::bsts_model(model = function(ss, y){ | ||
| bsts::AddSemilocalLinearTrend(ss, y = y) | ||
| }, ...)} | ||
| ) | ||
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| out <- compare_timeseries(obs_rts, obs_cases, models, | ||
| horizon = 7, samples = 10, | ||
| serial_interval = EpiSoon::example_serial_interval) | ||
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| test_that("Outputs have proper lenghts and names", { | ||
| expect_length(out, 4) | ||
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| expect_named(out, c("forecast_rts", "rt_scores", "forecast_cases", "case_scores")) | ||
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| # 'return_raw' version | ||
| out_raw <- compare_timeseries(obs_rts, obs_cases, models, | ||
| horizon = 7, samples = 10, | ||
| serial_interval = EpiSoon::example_serial_interval, | ||
| return_raw = TRUE) | ||
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| expect_length(out_raw, 6) | ||
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| expect_named(out_raw, c("forecast_rts", "rt_scores", "forecast_cases", | ||
| "case_scores", "raw_rt_forecast", "raw_case_forecast")) | ||
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| }) | ||
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| test_that("Outputs return results for all models", { | ||
| expect_identical(names(models), unique(out$forecast_rts$model)) | ||
| expect_equal(sum(is.na(out$forecast_rts)), 0) | ||
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| expect_identical(names(models), unique(out$rt_scores$model)) | ||
| expect_equal(sum(is.na(out$rt_scores)), 0) | ||
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| expect_identical(names(models), unique(out$forecast_cases$model)) | ||
| expect_equal(sum(is.na(out$forecast_cases)), 0) | ||
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| expect_identical(names(models), unique(out$case_scores$model)) | ||
| expect_equal(sum(is.na(out$case_scores)), 0) | ||
| }) |
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| # draw_from_si_prob | ||
| # This function returns result for requested days. It simply calls for | ||
| # serial_interval[days_ago] but checking first the 'days_ago' are in the | ||
| # interval. Otherwise, it returns 0. | ||
| # Things to test: | ||
| ## In tests | ||
| # - that the function return the proper result | ||
| # - that the result is of the proper class | ||
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| exampleResult <- draw_from_si_prob(c(1, 2, 4, 10), | ||
| EpiSoon::example_serial_interval) | ||
| # expectedResult <- EpiSoon::example_serial_interval[c(1, 2, 4, 10)] | ||
| test_that("The expected draw is obtained", { | ||
| # expect_equal(exampleResult, expectedResult) | ||
| expect_true(is.numeric(exampleResult)) | ||
| expect_length(exampleResult, 4) | ||
| }) |
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| ##------------------------------------------------------------ | ||
| context("Test of the function 'evaluate_model'.... testing inputs") | ||
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| sampled_obs <- EpiSoon::example_obs_rts %>% | ||
| dplyr::mutate(sample = 1) %>% | ||
| dplyr::bind_rows(EpiSoon::example_obs_rts %>% | ||
| dplyr::mutate(sample = 2)) | ||
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| sampled_cases <- EpiSoon::example_obs_cases %>% | ||
| dplyr::mutate(sample = 1) %>% | ||
| dplyr::bind_rows(EpiSoon::example_obs_cases %>% | ||
| dplyr::mutate(sample = 2)) | ||
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| a_model <- function(...) { | ||
| EpiSoon::bsts_model(model = function(ss, y) { | ||
| bsts::AddSemilocalLinearTrend(ss, y = y) | ||
| }, ...) | ||
| } | ||
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| test_that("Inputs with unequal lengths return error", { | ||
| sampled_cases_sub <- sampled_cases %>% filter(sample != 2) | ||
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| expect_error( | ||
| evaluate_model(sampled_obs, | ||
| sampled_cases_sub, | ||
| model = a_model, | ||
| horizon = 7, samples = 10, | ||
| serial_interval = EpiSoon::example_serial_interval), | ||
| "Must have the same number of Rt and case samples." | ||
| ) | ||
| }) | ||
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| context("Test of the function 'evaluate_model'.... testing outputs") | ||
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| test_that("Outputs have proper lenghts and names", { | ||
| out <- evaluate_model(sampled_obs, | ||
| sampled_cases, | ||
| model = a_model, | ||
| horizon = 7, samples = 10, | ||
| serial_interval = EpiSoon::example_serial_interval) | ||
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| expect_length(out, 4) | ||
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| expect_named(out, c("forecast_rts", "rt_scores", "forecast_cases", "case_scores")) | ||
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| # raw outputs added | ||
| out <- evaluate_model(sampled_obs, | ||
| sampled_cases, | ||
| model = a_model, | ||
| horizon = 7, samples = 10, | ||
| serial_interval = EpiSoon::example_serial_interval, | ||
| return_raw = TRUE) | ||
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| expect_length(out, 6) | ||
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| expect_named(out, | ||
| c("forecast_rts", "rt_scores", "forecast_cases", "case_scores", | ||
| "raw_rt_forecast", "raw_case_forecast")) | ||
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| }) |
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