tests/testthat/test-PCC.contam.R

In stemmatology: Stemmatological Analysis of Textual Traditions

context("PCC.contam")

test_that("works on numeric matrix input, or on pccConflicts or pccOverconflicting", {
  x = matrix(
    data = c(
      1,1,1,1,
      1,2,0,2,
      2,1,1,1,
      2,2,0,2,
      2,3,0,NA
    ),
    ncol = 5,
    nrow = 4,
    dimnames = list(
      c("VL1","VL2","VL3","VL4"),
      c("A","B","C","D","E")
    )
  )
  
  results = list(
    totalByMs = 
      structure(c(2, 1, 0, 1, 2, 1, 0, 1, -2, -1, 0, -1, -2, -1, 0, -1, -2, -1, 0, -1, -2, -1, 0, -1, -2, -1, 0, -1, -2, -1, 0, -1,-2, -1, 0, -1, -2, -1, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0), 
        .Dim = c(4L,12L), 
        .Dimnames = list(c("VL1", "VL2", "VL3", "VL4"), 
          c("Number of conflicts", "Centrality index", "d. confl. A", "d. centr. A", "d. confl. B", "d. centr. B", "d. confl. C", "d. centr. C", "d. confl. D", "d. centr. D", "d. confl. E", "d. centr. E")
          )),
  conflictsDifferences = structure(c(-2, -2, -2, -2, 0), 
    .Dim = c(5L, 1L), .Dimnames = list(
    c("A", "B", "C", "D", "E"), "Conflicts differences")),
  database = x)
  class(results) = "pccContam"
  
  # expect output as well, or create option verbose
  expect_equal(
    expect_output(
      expect_message(
        PCC.contam(x)
        )
      )
    , results)
  
  
  pccConflicts = PCC.conflicts(x)
  
  expect_output(expect_message(PCC.contam(pccConflicts)))
  
  expect_equal(
    expect_output(
      expect_message(
        PCC.contam(pccConflicts)
      )
    )
    , results)
  
  
  pccOverconflicting = PCC.overconflicting(pccConflicts, ask = FALSE, threshold = 2)
  
  expect_equal(
    expect_output(
      expect_message(
        PCC.contam(pccOverconflicting)
      )
    )
    , results)
  
})


test_that("works on character matrix input", {
  x = matrix(
    data = c(
      "1,2","1","1","1","1,2","1",
      "1","2","0","2",NA,"2",
      "2","1","1","1",NA,"2",
      "2","2","0","2",NA,"2",
      "2","3","0",NA,NA,"3"
    ),
    ncol = 5,
    nrow = 6,
    dimnames = list(
      c("VL1","VL2","VL3","VL4","VL5","VL6"),
      c("A","B","C","D","E")
    )
  )
  
  # Check if input properly verified
  expect_error(PCC.contam(x))
  
  # And now check correct result
  
  results = list(
    totalByMs = structure(
      c(
        6,
        1,
        0,
        1,
        3,
        1,
        2,
        0.2,
        0,
        0.2,
        1,
        0.2,
        -6,
        -1,
        0,
        -1,
        -3,
        -1,
        -2,
        -0.2,
        0,
        -0.2,
        -1,
        -0.2,
        -3,
        -1,
        0,
        -1,
        0,
        -1,
        0,
        -0.2,
        0,
        -0.2,
        1,
        -0.2,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        -2,
        -1,
        0,
        -1,
        0,
        0,
        0,
        -0.2,
        0,
        -0.2,
        2,
        0.133333333333333,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0
      ),
      .Dim = c(6L, 12L),
      .Dimnames = list(
        c("VL1", "VL2", "VL3",
          "VL4", "VL5", "VL6"),
        c(
          "Number of conflicts",
          "Centrality index",
          "d. confl. A",
          "d. centr. A",
          "d. confl. B",
          "d. centr. B",
          "d. confl. C",
          "d. centr. C",
          "d. confl. D",
          "d. centr. D",
          "d. confl. E",
          "d. centr. E"
        )
      )
    ), conflictsDifferences = structure(
      c(-6,-3, 0,-2, 0),
      .Dim = c(5L,1L),
      .Dimnames = list(c("A", "B", "C", "D", "E"), "Conflicts differences")
    ),
    database = x)
  
  class(results) = "pccContam"
  
  expect_equal(
    expect_output(
      expect_message(
        PCC.contam(x, alternateReadings = TRUE)
      )
    )
    , results)
  
})
# $conflictsDifferences
# Conflicts differences
# A                    -6
# B                    -3
# C                     0
# D                    -2
# E                     0

# TODO
# test_that("works on larger input", {
#   
# })