allelematch_1-amDataset.md
In amregtest: Runs Allelematch Regression Tests

See how an object of class amDataset is built:

Code
  print(miniExample)
Output
    sampleId knownIndividual             dismiss. LOC1a LOC1b LOC2a LOC2b
  1        1               A                 Rain    11    21    31    41
  2        2               A                drops    12    22    32    42
  3        3               B                 keep    13    23    33    43
  4        4               C  fallin' on my head     14    24   -88    44

Code
  miniDataset1 <- amDataset(miniExample)

Code
  print.amDataset(miniDataset1)
Output
  allelematch
  amDataset object
      sampleId knownIndividual        dismiss. LOC1a LOC1b LOC2a LOC2b
  AAA        1               A            Rain    11    21    31    41
  AAB        2               A           drops    12    22    32    42
  AAC        3               B            keep    13    23    33    43
  AAD        4               C fallin'onmyhead    14    24   -88    44

{
  "type": "list",
  "attributes": {
    "names": {
      "type": "character",
      "attributes": {},
      "value": ["index", "multilocus", "missingCode"]
    },
    "class": {
      "type": "character",
      "attributes": {},
      "value": ["amDataset"]
    }
  },
  "value": [
    {
      "type": "character",
      "attributes": {},
      "value": ["AAA", "AAB", "AAC", "AAD"]
    },
    {
      "type": "character",
      "attributes": {
        "dim": {
          "type": "integer",
          "attributes": {},
          "value": [4, 7]
        },
        "dimnames": {
          "type": "list",
          "attributes": {},
          "value": [
            {
              "type": "NULL"
            },
            {
              "type": "character",
              "attributes": {},
              "value": ["sampleId", "knownIndividual", "dismiss.", "LOC1a", "LOC1b", "LOC2a", "LOC2b"]
            }
          ]
        }
      },
      "value": ["1", "2", "3", "4", "A", "A", "B", "C", "Rain", "drops", "keep", "fallin'onmyhead", "11", "12", "13", "14", "21", "22", "23", "24", "31", "32", "33", "-88", "41", "42", "43", "44"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["-99"]
    }
  ]
}

Code
  miniDataset2 <- amDataset(miniExample, missingCode = "-88", indexColumn = "sampleId",
    metaDataColumn = "knownIndividual", ignoreColumn = "dismiss.")

Code
  print.amDataset(miniDataset2)
Output
  allelematch
  amDataset object
         LOC1a LOC1b LOC2a LOC2b
  1  A      11    21    31    41
  2  A      12    22    32    42
  3  B      13    23    33    43
  4    C    14    24   -88    44

{
  "type": "list",
  "attributes": {
    "names": {
      "type": "character",
      "attributes": {},
      "value": ["index", "metaData", "multilocus", "missingCode"]
    },
    "class": {
      "type": "character",
      "attributes": {},
      "value": ["amDataset"]
    }
  },
  "value": [
    {
      "type": "character",
      "attributes": {},
      "value": ["1", "2", "3", "4"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["A", "A", "B", "  C"]
    },
    {
      "type": "character",
      "attributes": {
        "dim": {
          "type": "integer",
          "attributes": {},
          "value": [4, 4]
        },
        "dimnames": {
          "type": "list",
          "attributes": {},
          "value": [
            {
              "type": "NULL"
            },
            {
              "type": "character",
              "attributes": {},
              "value": ["LOC1a", "LOC1b", "LOC2a", "LOC2b"]
            }
          ]
        }
      },
      "value": ["11", "12", "13", "14", "21", "22", "23", "24", "31", "32", "33", "-88", "41", "42", "43", "44"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["-88"]
    }
  ]
}

Code
  miniDataset3 <- amDataset(miniExample, missingCode = "-88", indexColumn = 1,
    metaDataColumn = 2, ignoreColumn = 3)

Code
  print.amDataset(miniDataset2)
Output
  allelematch
  amDataset object
         LOC1a LOC1b LOC2a LOC2b
  1  A      11    21    31    41
  2  A      12    22    32    42
  3  B      13    23    33    43
  4    C    14    24   -88    44

{
  "type": "list",
  "attributes": {
    "names": {
      "type": "character",
      "attributes": {},
      "value": ["index", "metaData", "multilocus", "missingCode"]
    },
    "class": {
      "type": "character",
      "attributes": {},
      "value": ["amDataset"]
    }
  },
  "value": [
    {
      "type": "character",
      "attributes": {},
      "value": ["1", "2", "3", "4"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["A", "A", "B", "  C"]
    },
    {
      "type": "character",
      "attributes": {
        "dim": {
          "type": "integer",
          "attributes": {},
          "value": [4, 4]
        },
        "dimnames": {
          "type": "list",
          "attributes": {},
          "value": [
            {
              "type": "NULL"
            },
            {
              "type": "character",
              "attributes": {},
              "value": ["LOC1a", "LOC1b", "LOC2a", "LOC2b"]
            }
          ]
        }
      },
      "value": ["11", "12", "13", "14", "21", "22", "23", "24", "31", "32", "33", "-88", "41", "42", "43", "44"]
    },
    {
      "type": "character",
      "attributes": {},
      "value": ["-88"]
    }
  ]
}

Different data types for arg to 'missingCode' give same result

Code
  ds1 <- amDataset(sample, missingCode = "NA")
Output
  allelematch:  NA data converted to NA

structure(list(index = c("AAA", "AAB", "AAC", "AAD"), multilocus = structure(c("11", 
"12", "13", "14", "21", "22", "23", "NA", "31", "32", "33", "NA", 
"41", "42", "43", "NA"), dim = c(4L, 4L), dimnames = list(NULL, 
    c("LOC1a", "LOC1b", "LOC2a", "LOC2b"))), missingCode = "NA"), class = "amDataset")

Code
  ds2 <- amDataset(sample, missingCode = NA)
Output
  allelematch:  NA data converted to NA

structure(list(index = c("AAA", "AAB", "AAC", "AAD"), multilocus = structure(c("11", 
"12", "13", "14", "21", "22", "23", "NA", "31", "32", "33", "NA", 
"41", "42", "43", "NA"), dim = c(4L, 4L), dimnames = list(NULL, 
    c("LOC1a", "LOC1b", "LOC2a", "LOC2b"))), missingCode = "NA"), class = "amDataset")