context("test-baseliner")
library(tbgeneratr)
library(magrittr)
testing_code <- quote({
expect_equal(class(input$adm), class(output))
expect_equal(length(unique(input$adm[[1]])), length(unique(output[[1]])))
expect_true(all(c("base_smear", "base_culture") %in% names(output)))
expect_true(length(unique(output[[1]])) == nrow(output))
expect_true(output$base_culture[output[[1]] == "XYZ1"] == "Positive")
expect_true(output$base_smear[output[[1]] == "XYZ1"] == "Scanty")
expect_true(is.na(output$base_culture[output[[1]] == "XYZ2"]))
expect_true(is.na(output$base_smear[output[[1]] == "XYZ2"]))
expect_true(output_days$base_culture[output_days[[1]] == "XYZ2"] == "Positive")
expect_true(output_days$base_smear[output_days[[1]] == "XYZ2"] == "3+")
expect_true(output$base_culture[output[[1]] == "XYZ3"] == "Positive")
expect_true(output$base_smear[output[[1]] == "XYZ3"] == "1+")
expect_true(output$base_culture[output[[1]] == "XYZ4"] == "Positive")
expect_true(output$base_smear[output[[1]] == "XYZ4"] == "3+")
expect_true(is.na(output$base_culture[output[[1]] == "XYZ5"]))
expect_true(is.na(output$base_smear[output[[1]] == "XYZ5"]))
})
# EpiInfo
input <- system.file("testdata", "baseliner_epi.rds",
package = "tbgeneratr") %>%
readRDS()
output <- baseliner(
adm = input$adm,
lab = input$lab,
baseline_test = "culture",
baseline_days = 90
) %>%
baseliner(lab = input$lab,
baseline_test = "smear",
baseline_days = 90)
output_days <- baseliner(
adm = input$adm,
lab = input$lab,
baseline_test = "culture",
baseline_days = 95
) %>%
baseliner(lab = input$lab,
baseline_test = "smear",
baseline_days = 95)
# test code
test_that("EpiInfo testing", eval(testing_code))
# koch 6
input <- system.file("testdata", "baseliner_k6.rds",
package = "tbgeneratr") %>%
readRDS()
output <- baseliner(
adm = input$adm,
lab = input$lab,
baseline_test = "culture",
baseline_days = 90
) %>%
baseliner(lab = input$lab,
baseline_test = "smear",
baseline_days = 90)
output_days <- baseliner(
adm = input$adm,
lab = input$lab,
baseline_test = "culture",
baseline_days = 95
) %>%
baseliner(lab = input$lab,
baseline_test = "smear",
baseline_days = 95)
# test code
test_that("Koch 6 testing", eval(testing_code))
# Grozny
input <- system.file("testdata", "baseliner_groz.rds",
package = "tbgeneratr") %>%
readRDS()
output <- baseliner(
adm = input$adm,
lab = input$lab,
baseline_test = "culture",
baseline_days = 90
) %>%
baseliner(lab = input$lab,
baseline_test = "smear",
baseline_days = 90)
output_days <- baseliner(
adm = input$adm,
lab = input$lab,
baseline_test = "culture",
baseline_days = 95
) %>%
baseliner(lab = input$lab,
baseline_test = "smear",
baseline_days = 95)
# test code
test_that("Grozny testing", eval(testing_code))
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