tests/testthat/test_subsetting.r

In rbiom: Read/Write, Transform, and Summarize 'BIOM' Data

library(slam)

biom <- readRDS("inputs/biom.rds")


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# Rarefaction
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context("Rarefaction")

biom <- rarefy(biom, 100)

test_that("Rarefaction", {
  expect_equal(biom, readRDS("outputs/rarefy.rds"))
  
  # matrix in, matrix out
  x  <- matrix(runif(100, 0, 1000), ncol=10)
  y  <- rarefy(x, depth=100)
  z  <- merge(reshape2::melt(x), reshape2::melt(y), by=c('Var1', 'Var2'))
  r2 <- summary(lm(value.x ~ value.y, data=z))$r.squared
  expect_is(y, "matrix")
  expect_gt(r2, .3)
  
  # simple_triplet_matrix in, simple_triplet_matrix out
  x  <- slam::as.simple_triplet_matrix(matrix(runif(100, 0, 1000), ncol=10))
  y  <- rarefy(x, depth=100)
  z  <- merge(
    reshape2::melt(as.matrix(x)), 
    reshape2::melt(as.matrix(y)), 
    by=c('Var1', 'Var2'))
  r2 <- summary(lm(value.x ~ value.y, data=z))$r.squared
  expect_is(y, "simple_triplet_matrix")
  expect_gt(r2, .3)
  
  remove("x", "y", "z", "r2")
  # ggplot(z, aes(x=value.x, y=value.y)) + geom_smooth(method = "lm") + geom_point()
})



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# Subset/Select
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context("Subset/Select")


ex1 <- subset(biom, Age > 30)
ex2 <- subset(biom, Body.Site %in% c("Saliva", "Stool"))
ex3 <- subset(biom, Age < 25 & BMI > 22)

test_that("Subsetting", {
  expect_equal(ex1, readRDS("outputs/subset_ex1.rds"))
  expect_equal(ex2, readRDS("outputs/subset_ex2.rds"))
  expect_equal(ex3, readRDS("outputs/subset_ex3.rds"))
})
remove("ex1", "ex2", "ex3")


ex1 <- select(biom, c("1S/~5B.", "DV%sB[?=S", ")p*PCn[="))
ex2 <- select(biom, c(32, 11, 28, 16, 46, 5))
ex3 <- select(biom, 1:50 %% 6 == 0)

test_that("Selecting", {
  expect_equal(ex1, readRDS("outputs/select_ex1.rds"))
  expect_equal(ex2, readRDS("outputs/select_ex2.rds"))
  expect_equal(ex3, readRDS("outputs/select_ex3.rds"))
})
remove("ex1", "ex2", "ex3")


remove("biom")