tests/testthat/test_checks.R

In rtrim: Trends and Indices for Monitoring Data

context("data checkers")

test_that("basic assertions",{
  expect_error(assert_positive(-1,"foo"),regexp = "foo")
  expect_error(assert_positive(0,"foo"),regexp = "foo")
  expect_true(assert_positive(1,"foo"))

  # expect_error(assert_increasing(c(3,1,4)) )
  # expect_true(assert_increasing(1:2))

  expect_error(assert_sufficient_counts(count=0:2,index = 1:3))
  expect_true(assert_sufficient_counts(count=1:3,index=1:3))
})


test_that("check_observations",{
  # model 3, no covariates
  d <- data.frame(year = 1:3, count=0:2)
  out <- check_observations(d,model=3)
  expect_false(out$sufficient)
  expect_equal(out$errors,list(year="1"))

  # model 3 with covariates
  d <- data.frame(count=rep(0:1,2), year=rep(1:2,each=2), cov = rep(1:2,2))
  out <- check_observations(d, model=3, covars="cov")
  expect_false(out$sufficient)
  target = list(cov=data.frame(year=factor(1:2),cov=factor(c(1,1),levels=1:2)))
  expect_equal(out$errors, target)

  # model 2, no covariates
  d <- data.frame(year=1:10, count=c(rep(1,7), rep(0,3)))
  out <- check_observations(d, model=2, changepoints = c(4,7))
  expect_false(out$sufficient)
  expect_equal(out$errors$changepoint, 7)

  # model 2, with covariates
  d <- data.frame(
    year=1:4
    , X = c("A","A","A","B")
    , count = c(1,1,1,0)
  )
  # browser()
  out <- check_observations(d, model=2, covars="X", changepoints=1)
  expect_false(out$sufficient)
  expect_equal(out$errors$X, data.frame(changepoint=factor(1), X=factor("B",levels=c("A","B")) ))
})


test_that("Sufficient data for piecewise linear trend model (Model 2)",{

  ## no covariates
  d <- data.frame(count=rep(0:10,2), site=rep(1:2,11), time=rep(1:11,each=2))
  expect_true(assert_plt_model(d$count, d$time, changepoints=c(1,4,10),covars=list()))
  expect_true(assert_plt_model(d$count, d$time, changepoints=integer(0),covars=list()))

  d$count[d$time>10] <- 0
  expect_error(assert_plt_model(d$count, d$time, changepoints=c(1,4,10),covars=list()),regexp="10")

  ## with covariates:
  d <- data.frame(
    count = c(0,1,7,3)
    , time = rep(1:2,each=2)
    , cov=c("a","b","a","a")
  )
  cpts <- 1
  d$piece <- pieces_from_changepoints(d$time, cpts)
  expect_error(assert_plt_model(d$count,d$time,changepoints=1, covars=list(cov=d$cov)))

  # time   : 1 2 3
  # count a: 2 7 0
  # count b: 1 3 2
  # chpts  : 1 2    # Fails, because covar 'a' has no data for chpt 2
  d <- data.frame(
    time  = c(1:3,        1:3),
    count = c(2,7,0,      1,3,2),
    cov   = c(rep("a",3), rep("b",3)))
  expect_error(assert_plt_model(d$count, d$time, changepoints=c(1,2), covars=list(cov=d$cov)))
})


test_that("Sufficient data for model 3 with covariates",{

  d <- data.frame(count = rep(0:1,2), time = rep(1:2,each=2), cov = rep(1:2,2))
  expect_error(assert_covariate_counts(d$count, d$time, d["cov"]),regexp="cov")
  d <- data.frame(count = rep(7:8,2),time = rep(1:2,each=2), cov = rep(1:2,2))
  expect_true(assert_covariate_counts(d$count, d$time, d["cov"]))

  # with errors in two covariates
  d <- data.frame(count = rep(0:1,2), time = rep(1:2,each=2)
                  , covA = rep(1:2,2)
                  , covB = rep(letters[1:2],2))
  expect_error(assert_covariate_counts(d$count, d$time, d[3:4]),regexp="covB")
  expect_true(assert_covariate_counts(d$count, d$time, data.frame()))
})


context("Autodelete")

test_that("autodelete w/o covariates",{

  # case nothing to delete
  time  <- c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
  count <- c(1, 1, 1, 1, 1, 1, 1, 1, 1,  1)
  cpts  <- c(         4,       7          )
  expect_equal(autodelete(count, time, cpts), cpts)

  # case something to delete
  time  <- c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
  count <- c(1, 1, 1, 1, 0, 0, 0, 1, 1,  1)
  cpts  <- c(         4,       7          ) # cpt 7 is removed to provide data to cpt 4
  expect_equal(autodelete(count, time, cpts), 4)
})

test_that("autodelete with covariates", {
  d <- data.frame(
    time = rep(1:10, times=2)
    , covar = rep(letters[1:2], each=10)
    , count = rep(1, 20)
  )

  # case all fine
  # BUG: there is no real time 1 for class b
  expect_equal(
    autodelete(count = d$count, time = d$time, changepoints=c(4,7),covars=list(cov=d$covar))
  , c(4,7)
  )

   #case delete 7
   d$count[8:10] <- 0
   expect_equal(
     autodelete(count = d$count, time = d$time, changepoints=c(4,7),covars=list(cov=d$covar))
     , 4
   )
  #

   expect_equal(
     autodelete(count = d$count, time = d$time, changepoints=c(1,4,7),covars=list(cov=d$covar))
     ,c(1, 4)
   )

})