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Table 5 Estimates of \({\hat{\eta }}\) over different time periods for the David et al. data

From: Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes

(a) Subject A
Phylum Class Family Genus All data Days 123–364
Actinobacteria Actinobacteria Actinomycetaceae Actinomyces 0.832 0.6665
Actinobacteria Actinobacteria Bifidobacteriaceae Bifidobacterium 0.3566 0.5527
Bacteroidetes Bacteroidia Bacteroidaceae Bacteroides 1.441 1.2507
Bacteroidetes Bacteroidia Prevotellaceae Prevotella 2.0256 1.9338
Firmicutes Bacilli Gemellaceae   1.1221 1.3865
Firmicutes Bacilli Carnobacteriaceae Granulicatella 1.6666 1.8486
Firmicutes Bacilli Streptococcaceae Streptococcus 1.3472 1.5587
Firmicutes Clostridia Lachnospiraceae   0.136 0.5283
Firmicutes Clostridia Lachnospiraceae   0.2726 0.8016
Firmicutes Clostridia Lachnospiraceae   0.5886 1.0314
Firmicutes Clostridia Lachnospiraceae Blautia 0.7966 0.785
Firmicutes Clostridia Lachnospiraceae Coprococcus 0.7619 0.7905
Firmicutes Clostridia Lachnospiraceae Dorea 0.8493 0.9004
Firmicutes Clostridia Lachnospiraceae Roseburia 0.1311 0.1414
Firmicutes Clostridia Lachnospiraceae [Ruminococcus] 0.5008 0.6914
Firmicutes Clostridia Ruminococcaceae   0.1105 0.4005
Firmicutes Clostridia Ruminococcaceae   0.6707 0.5662
Firmicutes Clostridia Ruminococcaceae Faecalibacterium 0.8978 0.8938
Firmicutes Clostridia Ruminococcaceae Ruminococcus 0.5539 0.7457
Firmicutes Clostridia Veillonellaceae Phascolarctobacterium 0.734 0.8391
Firmicutes Clostridia Veillonellaceae Veillonella 0.9389 0.9646
Firmicutes Erysipelotrichi Erysipelotrichaceae   0.7742 0.8541
Fusobacteria Fusobacteria Fusobacteriaceae Fusobacterium 2.0122 1.6443
Proteobacteria Gammaproteobacteria Enterobacteriaceae   0.3079 0.3638
Proteobacteria Gammaproteobacteria Pasteurellaceae Haemophilus 2.1665 2.6424
(b) Subject B
Phylum Class Family Genus All days Days 0–150 Days 160–318
Actinobacteria Actinobacteria Bifidobacteriaceae Bifidobacterium 0.9358 1.2257 1.2334
Bacteroidetes Bacteroidia Bacteroidaceae Bacteroides 0.6007 0.8103 0.3681
Firmicutes Bacilli Streptococcaceae Streptococcus 1.3091 2.78 0.785
Firmicutes Clostridia Lachnospiraceae   1.8332 0.6724 2.4082
Firmicutes Clostridia Lachnospiraceae   0.5128 0.9548 2.2174
Firmicutes Clostridia Lachnospiraceae   0.3539 0.733 0.3101
Firmicutes Clostridia Lachnospiraceae [Ruminococcus] 0.139 0.5218 1.4967
Firmicutes Clostridia Lachnospiraceae Blautia 1.0021 0.7035 0.3194
Firmicutes Clostridia Lachnospiraceae Coprococcus 0.6375 0.706 1.1748
Firmicutes Clostridia Lachnospiraceae Dorea 0.7622 0.7333 0.9792
Firmicutes Clostridia Lachnospiraceae Roseburia 3.9203 1.4014 5.3445
Firmicutes Clostridia Ruminococcaceae   0.7842 0.6013 5.3743
Firmicutes Clostridia Ruminococcaceae Faecalibacterium 0.7168 0.5899 1.0053
Firmicutes Clostridia Ruminococcaceae Ruminococcus 0.2663 0.6 0.2664
Firmicutes Clostridia Veillonellaceae Phascolarctobacterium 1.8373 1.2156 1.0925
Firmicutes Clostridia Veillonellaceae Veillonella 1.4537 1.4415 2.2837
Firmicutes Erysipelotrichi Erysipelotrichaceae   0.5073 0.5104 0.6201
Proteobacteria Gammaproteobacteria Enterobacteriaceae   4.9281 3.9415 5.3409
Proteobacteria Gammaproteobacteria Pasteurellaceae Haemophilus 1.2358 1.0513 2.0246
  1. Estimates for shorter time periods that differ from the estimate for the whole data by more than 2 standard errors are highlighted in italics. Entries in underline indicate that the estimates were close to 2 standard errors from the whole data estimate
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