Unit tests

DESCRIPTION

@@ -2,7 +2,7 @@ Package: SUMMER
 Type: Package
 Title: Spatio-Temporal Under-Five Mortality Methods for Estimation
 Version: 1.0.0
-Date: 2019-07-02
+Date: 2020-07-02
 Authors@R: c(
     person(given = "Bryan D", family = "Martin", email= "[email protected]", role = "aut"), 
     person(given = "Zehang R", family = "Li", email= "[email protected]", role = c("cre","aut")),
@@ -25,6 +25,6 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
 Additional_repositories: https://inla.r-inla-download.org/R/stable/
-Suggests: INLA, knitr, rmarkdown, readstata13, patchwork, rdhs, R.rsp
+Suggests: INLA, knitr, rmarkdown, readstata13, patchwork, rdhs, R.rsp, testthat (>= 2.1.0)
 VignetteBuilder: R.rsp, knitr
 NeedsCompilation: no

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(SUMMER)
+
+test_check("SUMMER")

tests/testthat/smoothDirect_run.R

@@ -0,0 +1,46 @@
+rm(list=ls())
+
+###########################################################
+##
+##  Test for smoothDirect
+##
+###########################################################
+
+library(SUMMER)
+data(DemoData)
+years <- levels(DemoData[[1]]$time)
+years.all <- c(years, "15-19")
+data_multi <- getDirectList(births = DemoData, years = years,
+regionVar = "region",  timeVar = "time", clusterVar = "~clustid+id",
+ageVar = "age", weightsVar = "weights", geo.recode = NULL)
+data <- aggregateSurvey(data_multi)
+
+###########################################################
+
+##
+## national model, rw2
+##  
+fit <- smoothDirect(data = data, Amat = NULL, time.model = "rw2",
+		year_label = years.all, year_range = c(1985, 2019), 
+		is.yearly=TRUE, m = 5)
+out1 <- getSmoothed(fit)
+
+
+##
+## subnational model, rw2
+##  
+fit <- smoothDirect(data = data, Amat = NULL, time.model = "rw2",
+		year_label = years.all, year_range = c(1985, 2019), 
+		is.yearly=TRUE, m = 5)
+out2 <- getSmoothed(fit)
+
+
+##
+## subnational model, period, rw2 and ar1 interaction
+##  
+fit <- smoothDirect(data = data, Amat = DemoMap$Amat, time.model = "rw2", st.time.model = "ar1",
+		year_label = years.all, year_range = c(1985, 2019), 
+		is.yearly=FALSE, type.st = 4)
+out3 <- getSmoothed(fit, Amat = DemoMap$Amat)
+
+save(data, years.all, out1, out2, out3, file="smoothDirect_regress.RData")

tests/testthat/test-expit.R

@@ -0,0 +1,15 @@
+context("test-expit")
+
+# The following functions are tested in this file:
+#     expit()
+#     logit()
+
+test_that("Expit works", {
+  expect_equal(expit(2), exp(2)/(1 + exp(2)))
+  expect_equal(expit(-2), exp(-2)/(1 + exp(-2)))
+})
+
+test_that("Logit works", {
+  expect_equal(logit(0.2), log(0.2/(1-0.2)))
+  expect_equal(logit(0.8), log(0.8/(1-0.8)))
+})

tests/testthat/test-smoothDirect.R

@@ -0,0 +1,71 @@
+context("test-smoothDirect")
+
+expect_5pd_prob <- function(x, y) {
+  raw_difference <- abs(x-y)  
+  return( expect_lte(max(raw_difference), 0.05) )
+}
+
+load("smoothDirect_regress.RData")
+
+
+## run tests
+test_that("Smooth Direct comparison: RW2 National", {
+
+
+	## national model, rw2
+	##  
+	fit <- smoothDirect(data = data, Amat = NULL, time.model = "rw2",
+			year_label = years.all, year_range = c(1985, 2019), 
+			is.yearly=TRUE, m = 5)
+	newout1 <- getSmoothed(fit)
+
+
+
+  # regression test to see if the results match expectation
+  expect_equal(newout1$region, out1$region)
+  expect_equal(newout1$years, out1$years)
+  expect_5pd_prob(newout1$upper, out1$upper)
+  expect_5pd_prob(newout1$lower, out1$lower)
+  expect_5pd_prob(newout1$median, out1$median)
+
+})
+
+
+
+test_that("Smooth Direct comparison: RW2 Subnational", {
+
+	##
+	## subnational model, rw2
+	##  
+	fit <- smoothDirect(data = data, Amat = NULL, time.model = "rw2",
+			year_label = years.all, year_range = c(1985, 2019), 
+			is.yearly=TRUE, m = 5)
+	newout2 <- getSmoothed(fit)
+
+	expect_equal(newout2$region, out2$region)
+	expect_equal(newout2$years, out2$years)
+	expect_5pd_prob(newout2$upper, out2$upper)
+	expect_5pd_prob(newout2$lower, out2$lower)
+	expect_5pd_prob(newout2$median, out2$median)
+
+ }) 
+
+
+test_that("Smooth Direct comparison: RW2 And AR1 Interaction", {
+
+	##
+	## subnational model, period, rw2 and ar1 interaction
+	##  
+	fit <- smoothDirect(data = data, Amat = DemoMap$Amat, time.model = "rw2", st.time.model = "ar1",
+			year_label = years.all, year_range = c(1985, 2019), 
+			is.yearly=FALSE, type.st = 4)
+	newout3 <- getSmoothed(fit, Amat = DemoMap$Amat)
+
+
+	expect_equal(newout3$region, out3$region)
+	expect_equal(newout3$years, out3$years)
+	expect_5pd_prob(newout3$upper, out3$upper)
+	expect_5pd_prob(newout3$lower, out3$lower)
+	expect_5pd_prob(newout3$median, out3$median)
+
+ })