tests/testthat/test-extract_svyrmir.R

In DjalmaPessoa/convey: Income Concentration Analysis with Complex Survey Samples

context("Svyrmir output survey.design and svyrep.design")

skip_on_cran()

library(laeken)
library(survey)

data(api)
dstrat1<-convey_prep(svydesign(id=~1,data=apistrat))
test_that("svyrmir works on unweighted designs",{
	svyrmir(~api00, design=dstrat1, age = ~emer)
})


data(eusilc) ; names( eusilc ) <- tolower( names( eusilc ) )

des_eusilc <- svydesign(ids = ~rb030, strata =~db040,  weights = ~rb050, data = eusilc)
des_eusilc <- convey_prep(des_eusilc)
des_eusilc_rep <-as.svrepdesign(des_eusilc, type= "bootstrap")

des_eusilc_rep <- convey_prep(des_eusilc_rep)

a1 <- svyrmir( ~eqincome , design = des_eusilc , age = ~age )

a2 <- svyby(~eqincome, by = ~hsize, design = subset( des_eusilc , hsize < 8 ), FUN = svyrmir, age = ~age )

b1 <- svyrmir( ~eqincome , design = des_eusilc_rep , age = ~age )

b2 <- svyby(~eqincome, by = ~hsize, design = subset( des_eusilc_rep, hsize < 8 ), FUN = svyrmir, age = ~age )

se_dif1 <- abs(SE(a1)-SE(b1))
se_diff2 <- max(abs(SE(a2)-SE(b2)))


test_that("output svyrmir",{
  expect_is(coef(a1),"numeric")
  expect_is(coef(a2), "numeric")
  expect_is(coef(b1),"numeric")
  expect_is(coef(b2),"numeric")
  expect_lte(se_dif1, coef(a1) * 0.05 ) # the difference between CVs should be less than 5% of the coefficient, otherwise manually set it
  expect_lte(se_diff2, max( coef(a2) ) * 0.1 ) # the difference between CVs should be less than 10% of the maximum coefficient, otherwise manually set it
  expect_equal(coef(a1), coef(b1))
  expect_equal(coef(a2), coef(b2))
  expect_is(SE(a1),"matrix")
  expect_is(SE(a2), "numeric")
  expect_is(SE(b1),"numeric")
  expect_is(SE(b2),"numeric")
  expect_lte(confint(a1)[1], coef(a1))
  expect_gte(confint(a1)[2],coef(a1))
  expect_lte(confint(b1)[1], coef(b1))
  expect_gte(confint(b1)[2], coef(b1))

  expect_equal(sum(confint(a2)[1:7,1]<= coef(a2)[1:7]),length(coef(a2)[1:7]))
  expect_equal(sum(confint(a2)[1:7,2]>= coef(a2)[1:7]),length(coef(a2)[1:7]))

  expect_equal(sum(confint(b2)[1:7,1]<= coef(b2)[1:7]),length(coef(b2)[1:7]))
  expect_equal(sum(confint(b2)[1:7,2]>= coef(b2)[1:7]),length(coef(b2)[1:7]))
})




	 # database-backed design
	library(RSQLite)
	library(DBI)
	dbfile <- tempfile()
	conn <- dbConnect( RSQLite::SQLite() , dbfile )
	dbWriteTable( conn , 'eusilc' , eusilc )

	dbd_eusilc <-
	svydesign(
	ids = ~rb030 ,
	strata = ~db040 ,
	weights = ~rb050 ,
	data="eusilc",
	dbname=dbfile,
	dbtype="SQLite"
	)
	dbd_eusilc <- convey_prep( dbd_eusilc )


	c1 <- svyrmir( ~ eqincome , design = dbd_eusilc , age = ~age )
	c2 <- svyby(~ eqincome, by = ~hsize, design = subset(dbd_eusilc,hsize<8), FUN = svyrmir , age = ~age )

	dbRemoveTable( conn , 'eusilc' )
		dbDisconnect( conn )

	test_that("database svyrmir",{
	  expect_equal(coef(a1), coef(c1))
	  expect_equal(coef(a2), coef(c2))
	  expect_equal(SE(a1), SE(c1))
	  expect_equal(SE(a2), SE(c2))
	})

# compare subsetted objects to svyby objects
sub_des <- svyrmir( ~eqincome , design = subset( des_eusilc , hsize == 1 ) , age = ~age )
sby_des <- svyby( ~eqincome, by = ~hsize, design = des_eusilc, FUN = svyrmir , age = ~age )
sub_rep <- svyrmir( ~eqincome , design = subset( des_eusilc_rep , hsize == 1 ) , age = ~age )
sby_rep <- svyby( ~eqincome, by = ~hsize, design = des_eusilc_rep, FUN = svyrmir , age = ~age )

test_that("subsets equal svyby",{
	expect_equal(as.numeric(coef(sub_des)), as.numeric(coef(sby_des))[1])
	expect_equal(as.numeric(coef(sub_rep)), as.numeric(coef(sby_rep))[1])
	expect_equal(as.numeric(SE(sub_des)), as.numeric(SE(sby_des))[1])
	expect_equal(as.numeric(SE(sub_rep)), as.numeric(SE(sby_rep))[1])

	# coefficients should match across svydesign & svrepdesign
	expect_equal(as.numeric(coef(sub_des)), as.numeric(coef(sby_rep))[1])

	# coefficients of variation should be within five percent
	cv_dif <- abs(cv(sub_des)-cv(sby_rep)[1])
	expect_lte(cv_dif,5)
})




# second run of database-backed designs #

	# database-backed design
	library(RSQLite)
	library(DBI)
	dbfile <- tempfile()
	conn <- dbConnect( RSQLite::SQLite() , dbfile )
	dbWriteTable( conn , 'eusilc' , eusilc )

	dbd_eusilc <-
		svydesign(
			ids = ~rb030 ,
			strata = ~db040 ,
			weights = ~rb050 ,
			data="eusilc",
			dbname=dbfile,
			dbtype="SQLite"
		)

	dbd_eusilc <- convey_prep( dbd_eusilc )

	# create a hacky database-backed svrepdesign object
	# mirroring des_eusilc_rep
	dbd_eusilc_rep <-
		svrepdesign(
			weights = ~ rb050,
			repweights = des_eusilc_rep$repweights ,
			scale = des_eusilc_rep$scale ,
			rscales = des_eusilc_rep$rscales ,
			type = "bootstrap" ,
			data = "eusilc" ,
			dbtype="SQLite" ,
			dbname = dbfile ,
			combined.weights = FALSE
		)

	dbd_eusilc_rep <- convey_prep( dbd_eusilc_rep )

	sub_dbd <- svyrmir( ~eqincome , design = subset( dbd_eusilc , hsize == 1 ) , age = ~age )
	sby_dbd <- svyby( ~eqincome, by = ~hsize, design = dbd_eusilc, FUN = svyrmir , age = ~age )
	sub_dbr <- svyrmir( ~eqincome , design = subset( dbd_eusilc_rep , hsize == 1 ) , age = ~age )
	sby_dbr <- svyby( ~eqincome, by = ~hsize, design = dbd_eusilc_rep, FUN = svyrmir , age = ~age )

	dbRemoveTable( conn , 'eusilc' )
		dbDisconnect( conn )


	# compare database-backed designs to non-database-backed designs
	test_that("dbi subsets equal non-dbi subsets",{
		expect_equal(coef(sub_des), coef(sub_dbd))
		expect_equal(coef(sub_rep), coef(sub_dbr))
		expect_equal(SE(sub_des), SE(sub_dbd))
		expect_equal(SE(sub_rep), SE(sub_dbr))
	})


	# compare database-backed subsetted objects to database-backed svyby objects
	test_that("dbi subsets equal dbi svyby",{
		expect_equal(as.numeric(coef(sub_dbd)), as.numeric(coef(sby_dbd))[1])
		expect_equal(as.numeric(coef(sub_dbr)), as.numeric(coef(sby_dbr))[1])
		expect_equal(as.numeric(SE(sub_dbd)), as.numeric(SE(sby_dbd))[1])
		expect_equal(as.numeric(SE(sub_dbr)), as.numeric(SE(sby_dbr))[1])
	})