R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("RUnit")
>
> options(warn=1)
>
> dirs <- 'unit'
>
> testFilePat <- ".*_test\\.R$"
>
> allSuite <- defineTestSuite(name="allSuite",
+ dirs=dirs,
+ testFileRegexp=testFilePat,
+ rngKind="default",
+ rngNormalKind="default"
+ )
>
> testData <- runTestSuite(allSuite)
Executing test function test_strep01 ...
classifier (depth 1): 149 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 463 between: 10563
findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20
classifier (depth 1): bkpt = 1.175
classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae
done successfully.
Executing test function test_strep02 ...
classifier (depth 1): 149 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 463 between: 10563
findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20
classifier (depth 1): bkpt = 1.175
classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae
done successfully.
Executing test function test_strep03 ...
classifier (depth 1): 149 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 471 between: 10555
findThreshold (depth 1): (out): D = 1.18 pmmi = 0.20
classifier (depth 1): bkpt = 1.181
classifier (depth 1): matches include S iniae
done successfully.
Executing test function test_bvseqs01 ...
findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species
findLowestRank: lowest defined rank: 12 (species)
classifyIter: starting rank is species
classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287]
classify (depth 1):
classifier (depth 1): 425 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 797 between: 89303
findThreshold (depth 1): (out): D = 0.09 pmmi = 0.05
classifier (depth 1): bkpt = 0.090
classifier (depth 1): matches include
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: FALSE
classify (depth 1): remainingGroupsLargeEnough: FALSE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): stopping at depth 1
classifyIter (depth 1): no matches - redefining groups at rank 11 (species_subgroup)
classifyIter (depth 2): 5 reference objects in 1 starting groups [578833]
classifyIter (depth 2): only one group met screening criteria - setting dStart to 0.0888
classify (depth 1):
classifier (depth 1): 5 elements in reference set
classifier (depth 1): setting D to dStart=0.089
classifier (depth 1): bkpt = 0.089
classifier (depth 1): matches include
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: FALSE
classify (depth 1): remainingGroupsLargeEnough: FALSE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): stopping at depth 1
classifyIter (depth 2): no matches - redefining groups at rank 10 (species_group)
classifyIter (depth 3): 60 reference objects in 6 starting groups [655183, 671232, 136843, 136845, 136846, 136841]
classify (depth 1):
classifier (depth 1): 60 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 520 between: 1250
findThreshold (depth 1): (out): D = 0.29 pmmi = 0.29
classifier (depth 1): bkpt = 0.286
classifier (depth 1): matches include
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: FALSE
classify (depth 1): remainingGroupsLargeEnough: FALSE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): stopping at depth 1
classifyIter (depth 3): no matches - redefining groups at rank 9 (genus)
classifyIter (depth 4): 422 reference objects in 35 starting groups [469, 160674, 561, 838, 816, 836, 2093, 2129, 1578, 46255, 1253, 1301, 1350, 1375, 1279, 1378, 168808, 848, 39948, 906, 1257, 165779, 150022, 162289, 1716, 1654, 184869, 2050, 2701, 1678, 419014, 84111, 1380, 357, 286]
classify (depth 1):
classifier (depth 1): 422 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 5585 between: 83246
findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22
classifier (depth 1): bkpt = 0.510
classifier (depth 1): matches include 286, 469
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: TRUE
classify (depth 1): remainingGroupsLargeEnough: TRUE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): running classify from depth 1
classify (depth 2):
classifier (depth 2): 54 elements in reference set
classifier (depth 2): running findThreshold, method="mutinfo"
findThreshold (depth 2): (in): method = mutinfo
findThreshold (depth 2): (in): within: 1026 between: 405
findThreshold (depth 2): (out): D = 0.33 pmmi = 0.85
classifier (depth 2): bkpt = 0.330
classifier (depth 2): matches include 469
classify (depth 2): threshIsValid: TRUE
classify (depth 2): moreThanOneMatch: FALSE
classify (depth 2): remainingGroupsLargeEnough: TRUE
classify (depth 2): remainingNotAllMatches: TRUE
classify (depth 2): stopping at depth 2
classifyIter (depth 4): matchCount = 1 --> breaking
============================================================
matches: 469
============================================================
--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.09 pmmi = 0.049
matches:
below above score match min median max
470 2 2 0.44 0 0.04 0.07 0.10
471 1 4 0.18 0 0.09 0.12 0.16
294 0 5 0.00 0 0.42 0.47 0.51
303 0 5 0.00 0 0.45 0.47 0.54
47880 0 5 0.00 0 0.46 0.47 0.50
70775 0 5 0.00 0 0.46 0.47 0.50
76759 0 5 0.00 0 0.45 0.48 0.51
78327 0 5 0.00 0 0.46 0.48 0.54
(... plus 85 groups not shown)
--------------- rank species_subgroup (depth 1) --------------------
thresh: prob =
classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09
method = user D = 0.09 pmmi =
matches:
below above score match min median max
578833 0 5 0 0 0.5 0.52 0.54
--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.29 pmmi = 0.287
matches:
below above score match min median max
136843 0 5 0 0 0.42 0.47 0.51
136845 0 30 0 0 0.45 0.48 0.62
136846 0 5 0 0 0.50 0.52 0.54
136841 0 5 0 0 0.57 0.59 0.62
655183 0 5 0 0 1.50 1.51 1.51
671232 0 10 0 0 1.62 1.66 1.71
--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.33 pmmi = 0.845
matches: 469
below above score match min median max
469 9 0 0.95 1 0.04 0.1 0.16
286 0 45 0.00 0 0.42 0.5 0.62
----------------------------------------------
============================================================
matches: Acinetobacter
============================================================
--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.09 pmmi = 0.049
matches:
below above score match min median max
Acinetobacter baumannii 2 2 0.44 0 0.04 0.07 0.10
Acinetobacter calcoaceticus 1 4 0.18 0 0.09 0.12 0.16
Pseudomonas fluorescens 0 5 0.00 0 0.42 0.47 0.51
Pseudomonas putida 0 5 0.00 0 0.45 0.47 0.54
Pseudomonas fulva 0 5 0.00 0 0.46 0.47 0.50
Pseudomonas plecoglossicida 0 5 0.00 0 0.46 0.47 0.50
Pseudomonas monteilii 0 5 0.00 0 0.45 0.48 0.51
Pseudomonas mosselii 0 5 0.00 0 0.46 0.48 0.54
(... plus 85 groups not shown)
--------------- rank species_subgroup (depth 1) --------------------
thresh: prob =
classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09
method = user D = 0.09 pmmi =
matches:
below above score match min median max
Pseudomonas stutzeri subgroup 0 5 0 0 0.5 0.52 0.54
--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.29 pmmi = 0.287
matches:
below above score match min median max
Pseudomonas fluorescens group 0 5 0 0 0.42 0.47 0.51
Pseudomonas putida group 0 30 0 0 0.45 0.48 0.62
Pseudomonas stutzeri group 0 5 0 0 0.50 0.52 0.54
Pseudomonas aeruginosa group 0 5 0 0 0.57 0.59 0.62
Lactobacillus casei group 0 5 0 0 1.50 1.51 1.51
Streptococcus anginosus group 0 10 0 0 1.62 1.66 1.71
--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.33 pmmi = 0.845
matches: Acinetobacter
below above score match min median max
Acinetobacter 9 0 0.95 1 0.04 0.1 0.16
Pseudomonas 0 45 0.00 0 0.42 0.5 0.62
----------------------------------------------
[1] "unit_output/test_bvseqs01.pdf"
Timing stopped at: 0.838 0.084 0.924
Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) :
could not find function "xyplot"
done successfully.
Executing test function test_bvseqs02 ...
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 5594 between: 83659
findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22
findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species
findLowestRank: lowest defined rank: 12 (species)
classifyIter: starting rank is species
classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287]
classify (depth 1):
classifier (depth 1): 425 elements in reference set
classifier (depth 1): setting D to dStart=0.510
classifier (depth 1): bkpt = 0.510
classifier (depth 1): matches include 294, 303, 470, 471, 47880, 70775, 78327
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: TRUE
classify (depth 1): remainingGroupsLargeEnough: TRUE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): running classify from depth 1
classify (depth 2):
classifier (depth 2): 34 elements in reference set
classifier (depth 2): running findThreshold, method="mutinfo"
findThreshold (depth 2): (in): method = mutinfo
findThreshold (depth 2): (in): within: 66 between: 495
findThreshold (depth 2): (out): D = 0.12 pmmi = 0.09
classifier (depth 2): bkpt = 0.121
classifier (depth 2): matches include 470
classify (depth 2): threshIsValid: TRUE
classify (depth 2): moreThanOneMatch: FALSE
classify (depth 2): remainingGroupsLargeEnough: TRUE
classify (depth 2): remainingNotAllMatches: TRUE
classify (depth 2): stopping at depth 2
classifyIter (depth 1): matchCount = 1 --> breaking
============================================================
matches: 470
============================================================
--------------- rank species (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.65 doffset = 0.5 dStart = NA
method = mutinfo D = 0.12 pmmi = 0.092
matches: 470
below above score match min median max
470 4 0 0.89 1 0.04 0.07 0.10
471 3 2 0.55 0 0.09 0.12 0.16
294 0 5 0.00 0 0.42 0.47 0.51
303 0 5 0.00 0 0.45 0.47 0.54
47880 0 5 0.00 0 0.46 0.47 0.50
70775 0 5 0.00 0 0.46 0.47 0.50
78327 0 5 0.00 0 0.46 0.48 0.54
----------------------------------------------
============================================================
matches: Acinetobacter baumannii
============================================================
--------------- rank species (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.65 doffset = 0.5 dStart = NA
method = mutinfo D = 0.12 pmmi = 0.092
matches: Acinetobacter baumannii
below above score match min median max
Acinetobacter baumannii 4 0 0.89 1 0.04 0.07 0.10
Acinetobacter calcoaceticus 3 2 0.55 0 0.09 0.12 0.16
Pseudomonas fluorescens 0 5 0.00 0 0.42 0.47 0.51
Pseudomonas putida 0 5 0.00 0 0.45 0.47 0.54
Pseudomonas fulva 0 5 0.00 0 0.46 0.47 0.50
Pseudomonas plecoglossicida 0 5 0.00 0 0.46 0.47 0.50
Pseudomonas mosselii 0 5 0.00 0 0.46 0.48 0.54
----------------------------------------------
[1] "unit_output/test_bvseqs02.pdf"
done successfully.
Executing test function test_bvseqs03 ...
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 6691 between: 82985
findThreshold (depth 1): (out): D = 0.48 pmmi = 0.24
findLowestRank: all defined ranks: superkingdom, superphylum, phylum, class, subclass, order, suborder, family, genus, species_group, species_subgroup, species
findLowestRank: lowest defined rank: 12 (species)
classifyIter: starting rank is species
classifyIter (depth 1): 425 reference objects in 93 starting groups [470, 471, 575, 562, 838_2, 28127, 838_3, 838_4, 838_7, 28125, 838_1, 28130, 838_6, 820, 28123, 2098, 2130, 134821, 1624, 1249, 1582, 47715, 1254, 97478, 1613, 1633, 181675, 1596, 147802, 109790, 47770, 1587, 1318, 1338, 1328, 1311, 1335, 1309, 1304, 1305, 1303, 28037, 1351, 1352, 33945, 87541, 1377, 1280, 29388, 1282, 1290, 1283, 1292, 186802_1, 187101, 40543, 849, 851, 186802_2, 186802_3, 39948_2, 39948_1, 906_2, 906_1, 1261, 33037, 33036, 33033, 1260, 33030, 33031, 38284, 103621, 184870, 2052, 2051, 2702, 1685, 216816, 1681, 419015, 82135, 1383, 358, 294, 303, 47885, 47880, 70775, 76759, 78327, 316, 287]
classify (depth 1):
classifier (depth 1): 425 elements in reference set
classifier (depth 1): setting D to dStart=0.480
classifier (depth 1): bkpt = 0.480
classifier (depth 1): matches include 294, 303, 470, 471, 47880, 70775
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: TRUE
classify (depth 1): remainingGroupsLargeEnough: TRUE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): running classify from depth 1
classify (depth 2):
classifier (depth 2): 29 elements in reference set
classifier (depth 2): running findThreshold, method="mutinfo"
findThreshold (depth 2): (in): method = mutinfo
findThreshold (depth 2): (in): within: 56 between: 350
findThreshold (depth 2): (out): D = 0.21 pmmi = 0.12
classifier (depth 2): bkpt = 0.210
classifier (depth 2): matches include 470, 471
classify (depth 2): threshIsValid: TRUE
classify (depth 2): moreThanOneMatch: TRUE
classify (depth 2): remainingGroupsLargeEnough: TRUE
classify (depth 2): remainingNotAllMatches: TRUE
classify (depth 2): running classify from depth 2
classify (depth 3):
classifier (depth 3): 9 elements in reference set
classifier (depth 3): running findThreshold, method="mutinfo"
findThreshold (depth 3): (in): method = mutinfo
findThreshold (depth 3): (in): within: 16 between: 20
findThreshold (depth 3): (out): D = NA pmmi = -0.04
classifier (depth 3): bkpt = NA
classifier (depth 3): matches include
classify (depth 3): threshIsValid: FALSE
classify (depth 3): moreThanOneMatch: FALSE
classify (depth 3): remainingGroupsLargeEnough: FALSE
classify (depth 3): remainingNotAllMatches: TRUE
classify (depth 3): stopping at depth 3
classify (depth 3): no matches on final iteration, returning previous result
classifyIter (depth 1): no matches - redefining groups at rank 11 (species_subgroup)
classifyIter (depth 2): 5 reference objects in 1 starting groups [578833]
classifyIter (depth 2): only one group met screening criteria - setting dStart to 0.0888
classify (depth 1):
classifier (depth 1): 5 elements in reference set
classifier (depth 1): setting D to dStart=0.089
classifier (depth 1): bkpt = 0.089
classifier (depth 1): matches include
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: FALSE
classify (depth 1): remainingGroupsLargeEnough: FALSE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): stopping at depth 1
classifyIter (depth 2): no matches - redefining groups at rank 10 (species_group)
classifyIter (depth 3): 60 reference objects in 6 starting groups [655183, 671232, 136843, 136845, 136846, 136841]
classify (depth 1):
classifier (depth 1): 60 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 520 between: 1250
findThreshold (depth 1): (out): D = 0.29 pmmi = 0.29
classifier (depth 1): bkpt = 0.286
classifier (depth 1): matches include
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: FALSE
classify (depth 1): remainingGroupsLargeEnough: FALSE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): stopping at depth 1
classifyIter (depth 3): no matches - redefining groups at rank 9 (genus)
classifyIter (depth 4): 422 reference objects in 35 starting groups [469, 160674, 561, 838, 816, 836, 2093, 2129, 1578, 46255, 1253, 1301, 1350, 1375, 1279, 1378, 168808, 848, 39948, 906, 1257, 165779, 150022, 162289, 1716, 1654, 184869, 2050, 2701, 1678, 419014, 84111, 1380, 357, 286]
classify (depth 1):
classifier (depth 1): 422 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 5585 between: 83246
findThreshold (depth 1): (out): D = 0.51 pmmi = 0.22
classifier (depth 1): bkpt = 0.510
classifier (depth 1): matches include 286, 469
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: TRUE
classify (depth 1): remainingGroupsLargeEnough: TRUE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): running classify from depth 1
classify (depth 2):
classifier (depth 2): 54 elements in reference set
classifier (depth 2): running findThreshold, method="mutinfo"
findThreshold (depth 2): (in): method = mutinfo
findThreshold (depth 2): (in): within: 1026 between: 405
findThreshold (depth 2): (out): D = 0.33 pmmi = 0.85
classifier (depth 2): bkpt = 0.330
classifier (depth 2): matches include 469
classify (depth 2): threshIsValid: TRUE
classify (depth 2): moreThanOneMatch: FALSE
classify (depth 2): remainingGroupsLargeEnough: TRUE
classify (depth 2): remainingNotAllMatches: TRUE
classify (depth 2): stopping at depth 2
classifyIter (depth 4): matchCount = 1 --> breaking
============================================================
matches: 469
============================================================
--------------- rank species (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.21 pmmi = 0.120
matches: 470, 471
below above score match min median max
471 5 0 0.91 1 0.09 0.12 0.16
470 4 0 0.89 1 0.04 0.07 0.10
294 0 5 0.00 0 0.42 0.47 0.51
303 0 5 0.00 0 0.45 0.47 0.54
47880 0 5 0.00 0 0.46 0.47 0.50
70775 0 5 0.00 0 0.46 0.47 0.50
--------------- rank species_subgroup (depth 1) --------------------
thresh: prob =
classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09
method = user D = 0.09 pmmi =
matches:
below above score match min median max
578833 0 5 0 0 0.5 0.52 0.54
--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.29 pmmi = 0.287
matches:
below above score match min median max
136843 0 5 0 0 0.42 0.47 0.51
136845 0 30 0 0 0.45 0.48 0.62
136846 0 5 0 0 0.50 0.52 0.54
136841 0 5 0 0 0.57 0.59 0.62
655183 0 5 0 0 1.50 1.51 1.51
671232 0 10 0 0 1.62 1.66 1.71
--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.33 pmmi = 0.845
matches: 469
below above score match min median max
469 9 0 0.95 1 0.04 0.1 0.16
286 0 45 0.00 0 0.42 0.5 0.62
----------------------------------------------
============================================================
matches: Acinetobacter
============================================================
--------------- rank species (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.21 pmmi = 0.120
matches: Acinetobacter baumannii, Acinetobacter calcoaceticus
below above score match min median max
Acinetobacter calcoaceticus 5 0 0.91 1 0.09 0.12 0.16
Acinetobacter baumannii 4 0 0.89 1 0.04 0.07 0.10
Pseudomonas fluorescens 0 5 0.00 0 0.42 0.47 0.51
Pseudomonas putida 0 5 0.00 0 0.45 0.47 0.54
Pseudomonas fulva 0 5 0.00 0 0.46 0.47 0.50
Pseudomonas plecoglossicida 0 5 0.00 0 0.46 0.47 0.50
--------------- rank species_subgroup (depth 1) --------------------
thresh: prob =
classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09
method = user D = 0.09 pmmi =
matches:
below above score match min median max
Pseudomonas stutzeri subgroup 0 5 0 0 0.5 0.52 0.54
--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.29 pmmi = 0.287
matches:
below above score match min median max
Pseudomonas fluorescens group 0 5 0 0 0.42 0.47 0.51
Pseudomonas putida group 0 30 0 0 0.45 0.48 0.62
Pseudomonas stutzeri group 0 5 0 0 0.50 0.52 0.54
Pseudomonas aeruginosa group 0 5 0 0 0.57 0.59 0.62
Lactobacillus casei group 0 5 0 0 1.50 1.51 1.51
Streptococcus anginosus group 0 10 0 0 1.62 1.66 1.71
--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.33 pmmi = 0.845
matches: Acinetobacter
below above score match min median max
Acinetobacter 9 0 0.95 1 0.04 0.1 0.16
Pseudomonas 0 45 0.00 0 0.42 0.5 0.62
----------------------------------------------
[1] "unit_output/test_bvseqs03.pdf"
Timing stopped at: 0.547 0.049 0.597
Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) :
could not find function "xyplot"
done successfully.
Executing test function test_strep01 ...
classify (depth 1):
classifier (depth 1): 149 elements in reference set
classifier (depth 1): running findThreshold, method="mutinfo"
findThreshold (depth 1): (in): method = mutinfo
findThreshold (depth 1): (in): within: 463 between: 10563
findThreshold (depth 1): (out): D = 1.17 pmmi = 0.20
classifier (depth 1): bkpt = 1.175
classifier (depth 1): matches include S mitis, S pneumoniae, S pseudopneumoniae
classify (depth 1): threshIsValid: TRUE
classify (depth 1): moreThanOneMatch: TRUE
classify (depth 1): remainingGroupsLargeEnough: TRUE
classify (depth 1): remainingNotAllMatches: TRUE
classify (depth 1): running classify from depth 1
classify (depth 2):
classifier (depth 2): 14 elements in reference set
classifier (depth 2): running findThreshold, method="mutinfo"
findThreshold (depth 2): (in): method = mutinfo
findThreshold (depth 2): (in): within: 42 between: 49
findThreshold (depth 2): (out): D = 0.46 pmmi = 0.30
classifier (depth 2): bkpt = 0.460
classifier (depth 2): matches include S mitis, S pseudopneumoniae
classify (depth 2): threshIsValid: TRUE
classify (depth 2): moreThanOneMatch: TRUE
classify (depth 2): remainingGroupsLargeEnough: TRUE
classify (depth 2): remainingNotAllMatches: TRUE
classify (depth 2): running classify from depth 2
classify (depth 3):
classifier (depth 3): 10 elements in reference set
classifier (depth 3): running findThreshold, method="mutinfo"
findThreshold (depth 3): (in): method = mutinfo
findThreshold (depth 3): (in): within: 36 between: 9
findThreshold (depth 3): (out): D = NA pmmi = -0.05
classifier (depth 3): bkpt = NA
classifier (depth 3): matches include
classify (depth 3): threshIsValid: FALSE
classify (depth 3): moreThanOneMatch: FALSE
classify (depth 3): remainingGroupsLargeEnough: FALSE
classify (depth 3): remainingNotAllMatches: TRUE
classify (depth 3): stopping at depth 3
classify (depth 3): no matches on final iteration, returning previous result
[1] "unit_output/test_strep01.pdf"
done successfully.
Executing test function test_actino ... done successfully.
Executing test function test_bvseqs ... done successfully.
Executing test function test_strep ... done successfully.
Executing test function test_ROC ... Timing stopped at: 0.008 0.001 0.008
Error in package.version("ROC") :
could not find function "package.version"
done successfully.
Executing test function test_findPMMI_strep01 ... done successfully.
Executing test function test_findPMMI_strep02 ... done successfully.
Executing test function test_findThreshold_strep01 ... done successfully.
Executing test function test_getThresh_01 ... done successfully.
Executing test function test_getThresh_02 ... done successfully.
Executing test function test_plotDistances_strep01 ... [1] "unit_output/test_plotDistances_strep01.pdf"
done successfully.
Executing test function test_plotDistances_strep02 ... [1] "unit_output/test_plotDistances_strep02.pdf"
done successfully.
Executing test function test_plotMutinfo_strep01 ... [1] "unit_output/test_plotMutinfo_strep01.pdf"
done successfully.
Executing test function test_partition_01 ... done successfully.
Executing test function test_bvseqs01 ...
============================================================
matches: 469
============================================================
--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.09 pmmi = 0.049
matches:
below above score match min median max
470 2 2 0.44 0 0.04 0.07 0.10
471 1 4 0.18 0 0.09 0.12 0.16
294 0 5 0.00 0 0.42 0.47 0.51
303 0 5 0.00 0 0.45 0.47 0.54
47880 0 5 0.00 0 0.46 0.47 0.50
70775 0 5 0.00 0 0.46 0.47 0.50
76759 0 5 0.00 0 0.45 0.48 0.51
78327 0 5 0.00 0 0.46 0.48 0.54
(... plus 85 groups not shown)
--------------- rank species_subgroup (depth 1) --------------------
thresh: prob =
classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09
method = user D = 0.09 pmmi =
matches:
below above score match min median max
578833 0 5 0 0 0.5 0.52 0.54
--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.29 pmmi = 0.287
matches:
below above score match min median max
136843 0 5 0 0 0.42 0.47 0.51
136845 0 30 0 0 0.45 0.48 0.62
136846 0 5 0 0 0.50 0.52 0.54
136841 0 5 0 0 0.57 0.59 0.62
655183 0 5 0 0 1.50 1.51 1.51
671232 0 10 0 0 1.62 1.66 1.71
--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.33 pmmi = 0.845
matches: 469
below above score match min median max
469 9 0 0.95 1 0.04 0.1 0.16
286 0 45 0.00 0 0.42 0.5 0.62
----------------------------------------------
============================================================
matches: Acinetobacter
============================================================
--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.09 pmmi = 0.049
matches:
below above score match min median max
Acinetobacter baumannii 2 2 0.44 0 0.04 0.07 0.10
Acinetobacter calcoaceticus 1 4 0.18 0 0.09 0.12 0.16
Pseudomonas fluorescens 0 5 0.00 0 0.42 0.47 0.51
Pseudomonas putida 0 5 0.00 0 0.45 0.47 0.54
Pseudomonas fulva 0 5 0.00 0 0.46 0.47 0.50
Pseudomonas plecoglossicida 0 5 0.00 0 0.46 0.47 0.50
Pseudomonas monteilii 0 5 0.00 0 0.45 0.48 0.51
Pseudomonas mosselii 0 5 0.00 0 0.46 0.48 0.54
(... plus 85 groups not shown)
--------------- rank species_subgroup (depth 1) --------------------
thresh: prob =
classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09
method = user D = 0.09 pmmi =
matches:
below above score match min median max
Pseudomonas stutzeri subgroup 0 5 0 0 0.5 0.52 0.54
--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.29 pmmi = 0.287
matches:
below above score match min median max
Pseudomonas fluorescens group 0 5 0 0 0.42 0.47 0.51
Pseudomonas putida group 0 30 0 0 0.45 0.48 0.62
Pseudomonas stutzeri group 0 5 0 0 0.50 0.52 0.54
Pseudomonas aeruginosa group 0 5 0 0 0.57 0.59 0.62
Lactobacillus casei group 0 5 0 0 1.50 1.51 1.51
Streptococcus anginosus group 0 10 0 0 1.62 1.66 1.71
--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.33 pmmi = 0.845
matches: Acinetobacter
below above score match min median max
Acinetobacter 9 0 0.95 1 0.04 0.1 0.16
Pseudomonas 0 45 0.00 0 0.42 0.5 0.62
----------------------------------------------
============================================================
matches: Acinetobacter
============================================================
--------------- rank species (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.09 pmmi = 0.049
matches:
below above score match min median max
Ac...r baumannii 2 2 0.44 0 0.04 0.07 0.10
Ac...lcoaceticus 1 4 0.18 0 0.09 0.12 0.16
Ps...fluorescens 0 5 0.00 0 0.42 0.47 0.51
Ps...onas putida 0 5 0.00 0 0.45 0.47 0.54
Ps...monas fulva 0 5 0.00 0 0.46 0.47 0.50
Ps...oglossicida 0 5 0.00 0 0.46 0.47 0.50
Ps...s monteilii 0 5 0.00 0 0.45 0.48 0.51
Ps...as mosselii 0 5 0.00 0 0.46 0.48 0.54
(... plus 85 groups not shown)
--------------- rank species_subgroup (depth 1) --------------------
thresh: prob =
classifer: minScore = 0.45 doffset = 0.5 dStart = 0.09
method = user D = 0.09 pmmi =
matches:
below above score match min median max
Ps...ri subgroup 0 5 0 0 0.5 0.52 0.54
--------------- rank species_group (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.29 pmmi = 0.287
matches:
below above score match min median max
Ps...scens group 0 5 0 0 0.42 0.47 0.51
Ps...utida group 0 30 0 0 0.45 0.48 0.62
Ps...tzeri group 0 5 0 0 0.50 0.52 0.54
Ps...inosa group 0 5 0 0 0.57 0.59 0.62
La...casei group 0 5 0 0 1.50 1.51 1.51
St...nosus group 0 10 0 0 1.62 1.66 1.71
--------------- rank genus (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.33 pmmi = 0.845
matches: Acinetobacter
below above score match min median max
Acinetobacter 9 0 0.95 1 0.04 0.1 0.16
Pseudomonas 0 45 0.00 0 0.42 0.5 0.62
----------------------------------------------
done successfully.
Executing test function test_strep01 ...
============================================================
matches: S mitis, S pseudopneumoniae
============================================================
--------------- rank (depth 1) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 1.17 pmmi = 0.199
matches: S mitis, S pneumoniae, S pseudopneumoniae
below above score match min median max
S mitis 9 0 0.95 1 0.00 0.38 0.58
S pneumoniae 4 0 0.89 1 0.56 0.60 0.97
S pseudopneumoniae 1 0 0.67 1 0.39 0.39 0.39
S australis 0 1 0.00 0 2.00 2.00 2.00
S infantis 0 2 0.00 0 2.23 2.42 2.61
S peroris 0 1 0.00 0 2.43 2.43 2.43
S sanguinis 0 5 0.00 0 3.74 4.04 5.73
S cristatus 0 1 0.00 0 4.61 4.61 4.61
(... plus 42 groups not shown)
--------------- rank (depth 2) --------------------
thresh: prob = 0.5
classifer: minScore = 0.45 doffset = 0.5 dStart = NA
method = mutinfo D = 0.46 pmmi = 0.300
matches: S mitis, S pseudopneumoniae
below above score match min median max
S mitis 7 2 0.74 1 0.00 0.38 0.58
S pseudopneumoniae 1 0 0.67 1 0.39 0.39 0.39
S pneumoniae 0 4 0.00 0 0.56 0.60 0.97
----------------------------------------------
done successfully.
>
> printTextProtocol(testData, showDetails=TRUE)
RUNIT TEST PROTOCOL -- Fri Oct 16 23:46:48 2020
***********************************************
Number of test functions: 22
Number of errors: 3
Number of failures: 0
1 Test Suite :
allSuite - 22 test functions, 3 errors, 0 failures
ERROR in test_bvseqs01: Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) :
could not find function "xyplot"
ERROR in test_bvseqs03: Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) :
could not find function "xyplot"
ERROR in test_ROC: Error in package.version("ROC") :
could not find function "package.version"
Details
***************************
Test Suite: allSuite
Test function regexp: ^test.+
Test file regexp: .*_test\.R$
Involved directory:
unit
---------------------------
Test file: unit/classifier_test.R
test_strep01: (3 checks) ... OK (0.08 seconds)
test_strep02: (3 checks) ... OK (0.04 seconds)
test_strep03: (3 checks) ... OK (0.05 seconds)
---------------------------
Test file: unit/classifyIter_test.R
test_bvseqs01: ERROR !!
Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) :
could not find function "xyplot"
test_bvseqs02: (0 checks) ... OK (0.51 seconds)
test_bvseqs03: ERROR !!
Error in xyplot(x ~ y, data = data.frame(x = 1:10, y = 1:10)) :
could not find function "xyplot"
---------------------------
Test file: unit/classify_test.R
test_strep01: (0 checks) ... OK (0.3 seconds)
---------------------------
Test file: unit/data_test.R
test_actino: (2 checks) ... OK (0.01 seconds)
test_bvseqs: (2 checks) ... OK (0.03 seconds)
test_strep: (2 checks) ... OK (0.01 seconds)
---------------------------
Test file: unit/dependencies_test.R
test_ROC: ERROR !!
Error in package.version("ROC") :
could not find function "package.version"
---------------------------
Test file: unit/findThreshold_test.R
test_findPMMI_strep01: (0 checks) ... OK (0.06 seconds)
test_findPMMI_strep02: (0 checks) ... OK (0.06 seconds)
test_findThreshold_strep01: (1 checks) ... OK (0.05 seconds)
test_getThresh_01: (2 checks) ... OK (0 seconds)
test_getThresh_02: (4 checks) ... OK (0 seconds)
test_plotDistances_strep01: (0 checks) ... OK (0.1 seconds)
test_plotDistances_strep02: (0 checks) ... OK (0.29 seconds)
test_plotMutinfo_strep01: (0 checks) ... OK (0.19 seconds)
---------------------------
Test file: unit/partition_test.R
test_partition_01: (2 checks) ... OK (0.02 seconds)
---------------------------
Test file: unit/print_test.R
test_bvseqs01: (0 checks) ... OK (0.36 seconds)
test_strep01: (0 checks) ... OK (0.07 seconds)
>
> #q(runLast=FALSE)
>
> proc.time()
user system elapsed
4.015 0.371 4.409
