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metadata_full

Metadata for Microbiome Samples

Bundled with DspikeIn · exported, loads via data()

Class
data.frame
Dimensions
312 × 46
Missing
287
Format
rda · xz
version 3 · 24 KB
File
data/metadata_full.rda
Fingerprint
fb1c4882
Format documented
Yes
Source
Source not stated
About this object
A table with named columnsA bordered table: a header band ruled off from the body with an empty slot over each column where its name goes, and rows of cells under it that share every edge. Nothing is in any of them.

Equal-length columns presented as a table, R's standard rectangular format. R object catalogue

Columns
Column
Type
Distinct
Missing
Summary
sample.id
character
312
0
13 – 23 characters
Total_Reads_total
integer
311
0
2 – 150395mean 3.457e+4
Min.
2
1st Qu.
18162.8
Median
25200
Mean
34569.4
3rd Qu.
38598
Max.
150395
Std. dev
27190.1
Skewness
1.627
Kurtosis
2.307
Outliers
420 low · 42 high
Total_Reads_spiked
integer
206
0
0 – 74210mean 4349
Min.
0
1st Qu.
14.75
Median
133
Mean
4349.03
3rd Qu.
592.75
Max.
74210
Std. dev
13353.8
Skewness
3.546
Kurtosis
11.89
Zeros
66
Outliers
520 low · 52 high
Percentage
numeric
247
0
0 – 76.7818mean 7.524
Min.
0
1st Qu.
0.0977
Median
0.6547
Mean
7.5235
3rd Qu.
2.6065
Max.
76.7818
Std. dev
17.4514
Skewness
2.668
Kurtosis
5.986
Zeros
66
Outliers
530 low · 53 high
Result
character
2
0
6 characters
beta.distances
numeric
310
0
0 – 0.9594mean 0.6149
Min.
0
1st Qu.
0.6059
Median
0.6394
Mean
0.6149
3rd Qu.
0.6872
Max.
0.9594
Std. dev
0.1397
Skewness
-2.099
Kurtosis
5.757
Zeros
2
Outliers
3229 low · 3 high
Observed
integer
244
0
1 – 1174mean 287.8
Min.
1
1st Qu.
83.75
Median
236
Mean
287.788
3rd Qu.
439
Max.
1174
Std. dev
226.298
Skewness
0.8817
Kurtosis
0.2752
Outliers
10 low · 1 high
Chao1
integer
244
0
1 – 1174mean 287.8
Min.
1
1st Qu.
83.75
Median
236
Mean
287.788
3rd Qu.
439
Max.
1174
Std. dev
226.298
Skewness
0.8817
Kurtosis
0.2752
Outliers
10 low · 1 high
ACE
integer
244
0
1 – 1174mean 287.8
Min.
1
1st Qu.
83.75
Median
236
Mean
287.788
3rd Qu.
439
Max.
1174
Std. dev
226.298
Skewness
0.8817
Kurtosis
0.2752
Outliers
10 low · 1 high
se.ACE
numeric
308
0
0 – 14.068mean 7.282
Min.
0
1st Qu.
4.4815
Median
7.4582
Mean
7.282
3rd Qu.
9.8287
Max.
14.068
Std. dev
3.1321
Skewness
-0.0722
Kurtosis
-0.8823
Zeros
2
Shannon
numeric
312
0
0 – 5.7216mean 3.201
Min.
0
1st Qu.
2.2585
Median
3.1846
Mean
3.2006
3rd Qu.
4.3394
Max.
5.7216
Std. dev
1.2947
Skewness
-0.1983
Kurtosis
-0.9684
Zeros
1
Simpson
numeric
312
0
0 – 0.9906mean 0.8377
Min.
0
1st Qu.
0.7931
Median
0.8823
Mean
0.8377
3rd Qu.
0.9644
Max.
0.9906
Std. dev
0.1705
Skewness
-1.845
Kurtosis
3.883
Zeros
1
Outliers
2121 low · 0 high
InvSimpson
numeric
312
0
1 – 106.032mean 19.16
Min.
1
1st Qu.
4.8338
Median
8.495
Mean
19.1644
3rd Qu.
28.1291
Max.
106.032
Std. dev
21.0815
Skewness
1.603
Kurtosis
2.077
Outliers
180 low · 18 high
X16S.biosample
integer
312
0
3286 – 21490mean 1.82e+4
Min.
3286
1st Qu.
20416.8
Median
20590.5
Mean
18204.8
3rd Qu.
20764.2
Max.
21490
Std. dev
6083.71
Skewness
-2.008
Kurtosis
2.054
Outliers
6945 low · 24 high
dna.biosample
integer
288
24
3063 – 19941mean 1.719e+4
Min.
3063
1st Qu.
19680.8
Median
19752.5
Mean
17186.2
3rd Qu.
19824.2
Max.
19941
Std. dev
6048.72
Skewness
-1.883
Kurtosis
1.552
Outliers
4545 low · 0 high
Longest gap
24
data.type
character
1
24
12 characters
ampliconlibrary.quantification.ng.ul
numeric
49
24
0.336 – 53mean 28.35
Min.
0.336
1st Qu.
25
Median
28
Mean
28.3484
3rd Qu.
32.25
Max.
53
Std. dev
9.0924
Skewness
-0.3527
Kurtosis
1.18
Outliers
3923 low · 16 high
Longest gap
24
plate.ID
character
5
24
9 – 20 characters
well.location
character
96
24
2 – 3 characters
Env.broad.scale
character
6
0
3 – 14 characters
Host.taxon
character
77
0
5 – 28 characters
Host.genus
character
42
0
5 – 14 characters
Host.species
character
73
0
5 – 15 characters
Animal.type
character
11
0
4 – 11 characters
Animal.ecomode
character
10
0
5 – 29 characters
Clade.Order
character
8
0
5 – 13 characters
Family
character
26
0
5 – 16 characters
Diet
character
7
0
5 – 19 characters
Diet.Detailed
character
22
0
5 – 43 characters
Habitat
character
18
0
5 – 15 characters
Metamorphosis
character
5
0
5 – 15 characters
Reproduction
character
5
1
5 – 13 characters
Ecoregion.III
character
11
71
5 – 31 characters
Ecoregion.IV
character
17
95
5 – 34 characters
Site
character
42
0
5 – 50 characters
sample.name
character
276
0
5 – 13 characters
biosample.parent
integer
312
0
3063 – 21464mean 1.75e+4
Min.
3063
1st Qu.
19686.8
Median
19764.5
Mean
17499.2
3rd Qu.
19842.2
Max.
21464
Std. dev
5911.7
Skewness
-1.995
Kurtosis
2.029
Outliers
6945 low · 24 high
data.type.1
character
1
0
12 characters
ampliconlibrary.quantification.ng.ul.1
numeric
55
0
0.336 – 53mean 27.88
Min.
0.336
1st Qu.
25
Median
28
Mean
27.8828
3rd Qu.
32
Max.
53
Std. dev
9.4088
Skewness
-0.5023
Kurtosis
1.251
Outliers
4828 low · 20 high
plate.ID.1
character
6
0
9 – 27 characters
well.location.1
character
96
0
2 – 3 characters
sample.or.blank
character
2
0
5 – 6 characters
sample.spiked.blank
character
3
0
5 – 6 characters
spiked.volume
integer
3
0
0 – 2mean 1.548
Min.
0
1st Qu.
1
Median
2
Mean
1.5481
3rd Qu.
2
Max.
2
Std. dev
0.7464
Skewness
-1.274
Kurtosis
-0.0174
Zeros
48
swab.presence
integer
2
0
0 – 1mean 0.1474
Min.
0
1st Qu.
0
Median
0
Mean
0.1474
3rd Qu.
0
Max.
1
Std. dev
0.3551
Skewness
1.979
Kurtosis
1.924
Zeros
266
MK.spike
integer
2
0
0 – 1mean 0.8462
Min.
0
1st Qu.
1
Median
1
Mean
0.8462
3rd Qu.
1
Max.
1
Std. dev
0.3614
Skewness
-1.91
Kurtosis
1.652
Zeros
48
Version history
VersionReleasedSizeChangeStored asConfidence
3.232026-04-28312 × 46Unchangedrda · xz
version 3 · 24 KB
exact
3.222025-10-29312 × 46–rda · xz
version 3 · 24 KB
exact

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