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LOG_tickpath.txt
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[1] "## Original number of rows: "
[1] 119836
[1] "## Original number of rows (NA test results removed): "
[1] 77040
[1] "## Samples that did not pass quality checks: "
[1] uid batchID
<0 rows> (or 0-length row.names)
[1] "## Batches NOT found in quality file: "
[1] "NEON_20180504" "NEON_20191210" "NEON_20170831"
[1] "## uids are unique?: TRUE"
[1] "## Which variables are missing data?: "
domainID siteID plotID decimalLatitude decimalLongitude plotType
FALSE FALSE FALSE FALSE FALSE FALSE
nlcdClass elevation collectDate subsampleID batchID testingID
FALSE FALSE FALSE FALSE FALSE FALSE
testPathogenName
TRUE
uid namedLocation collectDate sampleCondition
10 e173c1e7-938f-4412-82c6-38c931fa28e3 HARV_001.tickPlot.tck 2014-07-14T17:53Z Sample incomplete
remarks
10 Sample incomplete
[1] "## Sample conditions: "
Handling error OK Sample incomplete
2 119833 1
uid namedLocation collectDate sampleCondition
1 963b40c8-2e2f-4a4d-b665-e2a7c3745c08 HARV_001.tickPlot.tck 2014-06-02T16:10Z Handling error
3 f6825133-768d-4b37-82f8-ea3ac19891bb HARV_001.tickPlot.tck 2014-06-02T16:10Z Handling error
10 e173c1e7-938f-4412-82c6-38c931fa28e3 HARV_001.tickPlot.tck 2014-07-14T17:53Z Sample incomplete
remarks
1 Possibly mixed with HARV_001.20140602.IXOSCA.N.006
3 Possibly mixed with HARV_001.20140602.IXOSCA.N.005
10 Sample incomplete
[1] "## Number of test results that are NA: "
[1] 42796
[1] "## HardTick DNA Quality: "
testPathogenName
testResult HardTick DNA Quality
Positive 8559
[1] uid namedLocation collectDate sampleCondition remarks
<0 rows> (or 0-length row.names)
[1] "## Site x year for all tested ticks: "
year
siteID 2014 2015 2016 2017 2018
BLAN 0 0 40 81 30
DELA 0 2 0 0 7
HARV 9 42 0 74 53
KONA 0 0 0 14 0
KONZ 0 7 122 28 96
LENO 0 0 29 0 34
MLBS 0 0 0 0 1
ORNL 241 0 306 407 1225
OSBS 209 80 574 320 304
SCBI 195 0 70 114 153
SERC 0 0 121 324 473
TALL 240 187 216 421 136
TREE 0 0 117 112 121
UKFS 0 257 328 361 287
[1] "## Site x year for Ambame only: "
year
siteID 2014 2015 2016 2017 2018
BLAN 0 0 3 2 15
DELA 0 2 0 0 7
KONA 0 0 0 14 0
KONZ 0 7 122 28 96
LENO 0 0 28 0 34
ORNL 237 0 283 404 1210
OSBS 209 80 574 320 304
SCBI 37 0 11 80 91
SERC 0 0 61 242 343
TALL 240 187 216 421 136
UKFS 0 257 328 361 287
[1] "## Site x year for Ixosca only: "
year
siteID 2014 2015 2016 2017 2018
BLAN 0 0 37 79 15
HARV 9 42 0 74 53
LENO 0 0 1 0 0
MLBS 0 0 0 0 1
ORNL 4 0 23 3 15
SCBI 158 0 59 34 62
SERC 0 0 60 82 130
TREE 0 0 117 112 121
[1] "## Plot x year: "
year
plotID 2014 2015 2016 2017 2018
BLAN_005 0 0 39 78 30
BLAN_012 0 0 1 2 0
BLAN_015 0 0 0 1 0
DELA_005 0 0 0 0 1
DELA_008 0 2 0 0 6
HARV_001 9 0 0 35 5
HARV_002 0 0 0 0 9
HARV_004 0 25 0 18 1
HARV_006 0 0 0 3 1
HARV_020 0 8 0 5 0
HARV_022 0 6 0 11 32
HARV_026 0 3 0 2 5
KONA_002 0 0 0 7 0
KONA_003 0 0 0 6 0
KONA_019 0 0 0 1 0
KONZ_001 0 0 5 0 4
KONZ_002 0 0 7 0 0
KONZ_004 0 0 0 6 0
KONZ_007 0 0 0 1 0
KONZ_009 0 0 5 0 0
KONZ_025 0 7 105 21 92
LENO_002 0 0 2 0 3
LENO_003 0 0 20 0 1
LENO_004 0 0 0 0 13
LENO_015 0 0 0 0 2
LENO_023 0 0 4 0 2
LENO_042 0 0 3 0 13
MLBS_004 0 0 0 0 1
ORNL_002 88 0 64 124 714
ORNL_003 7 0 33 30 40
ORNL_007 27 0 102 42 57
ORNL_008 95 0 46 44 118
ORNL_009 13 0 36 29 283
ORNL_040 11 0 25 138 13
OSBS_001 16 0 140 13 273
OSBS_003 26 32 144 117 0
OSBS_004 2 0 4 2 1
OSBS_005 160 48 244 188 19
OSBS_022 5 0 42 0 0
OSBS_048 0 0 0 0 11
SCBI_002 48 0 21 14 36
SCBI_005 7 0 5 4 6
SCBI_006 4 0 1 0 7
SCBI_007 62 0 9 8 34
SCBI_013 69 0 34 74 66
SCBI_039 5 0 0 14 4
SERC_001 0 0 31 41 65
SERC_002 0 0 38 125 213
SERC_005 0 0 10 62 35
SERC_006 0 0 18 49 58
SERC_012 0 0 24 44 41
SERC_023 0 0 0 3 61
TALL_001 35 16 22 32 29
TALL_002 155 24 36 265 49
TALL_003 24 18 10 0 0
TALL_006 5 6 20 6 0
TALL_008 21 122 128 118 58
TALL_016 0 1 0 0 0
TREE_007 0 0 27 15 31
TREE_015 0 0 3 3 7
TREE_017 0 0 28 39 60
TREE_019 0 0 50 41 20
TREE_022 0 0 9 14 3
UKFS_001 0 212 176 109 106
UKFS_002 0 5 23 16 42
UKFS_003 0 21 59 160 61
UKFS_004 0 19 69 72 74
UKFS_018 0 0 0 0 3
UKFS_030 0 0 1 4 1
[1] "## Which species was tested for which pathogens: "
species
testPathogenName AMBAME IXOSCA
Anaplasma phagocytophilum 7277 1282
Babesia microti 37 1245
Borrelia burgdorferi 0 9
Borrelia burgdorferi sensu lato 37 1245
Borrelia lonestari 7240 37
Borrelia mayonii 37 1245
Borrelia miyamotoi 37 1245
Borrelia sp. 7277 1282
Ehrlichia chaffeensis 7240 37
Ehrlichia ewingii 7240 37
Ehrlichia muris-like 37 1245
Francisella tularensis 7240 37
HardTick DNA Quality 7277 1282
Ixodes pacificus 7277 1282
Rickettsia rickettsii 7240 37