
Alistipes_finegoldii
[  0   4  35  37  46  49  92 110 118 129 153]
[ 327  697  163  151  165   63  604 2340 1859 2311 1681]
[2482 2500 1748 1462  743  388  968 2500 2021 2500 2139]
[0.13174859 0.2788     0.09324943 0.10328317 0.22207268 0.16237113
 0.62396694 0.936      0.91984166 0.9244     0.78588125]
Birth: 0
Death: 10
20-70: 5 7
mid: 6
pre-post-abx: 5 7
Post-abx fit test: p= 0.342657342657
Post-fixation fit test: p= 0.345654345654
Pre-fixation fit test: p= 0.514485514486
Jorde Ryman scores
[ 2.02461877e-02  4.63102063e-03 -1.61859117e-04  7.70096743e-03
  3.47508329e-03  6.91394650e-03  1.43811192e-03 -1.09334018e-04
 -8.12126017e-05  9.94101179e-05]
All Ne: 226.488655315
Post-fixation Ne: -32917.6557569
Pre-fixation Ne: 139.309138467
Fixation time: 61
Fixation Ne: 61.0
Effective generations per day: 2.0
Nhat: 122
[  0.   8.  70.  74.  92.  98. 184. 220. 236. 258. 306.]
All Ne: 122.0
Post Ne: 969.080446364
Pre Ne: 122.0
Postpre Ne: 193.35696948
all
Post pvalue: 0.158584141586
Pre pvalue: 0.259074092591
Both pvalue: 0.0575942405759
joint
Post pvalue: 0.20497950205
Pre pvalue: 0.220777922208
Both pvalue: 0.0870912908709
separate
Post pvalue: 0.122487751225
Pre pvalue: 0.253474652535
Both pvalue: 0.0993900609939

Bacteroides_coprocola_blue
[  0   4  10  25  35  37  46  49  67  69  72  74  77  80  92 110 118 129 153]
[   3 1796   26   35  544  354 1953 1897  737  848 1602 2191 2279 2311 2229 2267 2359  236 2497]
[ 629 2500  789  161 2500 1141 2500 2500 2500 2500 2500 2500 2500 2500
 2500 2500 2500  247 2500]
[0.00476948 0.7184     0.03295311 0.2173913  0.2176     0.31025416
 0.7812     0.7588     0.2948     0.3392     0.6408     0.8764
 0.9116     0.9244     0.8916     0.9068     0.9436     0.95546559
 0.9988    ]
Birth: 0
Death: 18
20-70: 2 6
mid: 5
pre-post-abx: 2 9
Post-abx fit test: p= 0.230769230769
Post-fixation fit test: p= 0.656343656344
Pre-fixation fit test: p= 0.581418581419
Jorde Ryman scores
[ 1.81926795e-01  1.08184995e-01  1.46034773e-02 -6.58106912e-04
  1.12817716e-02  1.94261090e-02 -2.16815510e-04  1.01932729e-02
  1.71733929e-03  3.05252106e-02  8.39212165e-03 -2.17700999e-04
 -2.61879290e-04 -5.75852274e-05 -4.30200407e-05 -8.63037916e-05
 -4.05690052e-04 -1.83121374e-04]
All Ne: 46.8602501392
Post-fixation Ne: 243.132380478
Pre-fixation Ne: 6.89389425322
Fixation time: 36
Fixation Ne: 36.0
Effective generations per day: 3.0
Nhat: 108
[  0.  12.  30.  75. 105. 111. 138. 147. 201. 207. 216. 222. 231. 240. 276. 330. 354. 387. 459.]
All Ne: 108.0
Post Ne: 271.283734603
Pre Ne: 108.0
Postpre Ne: 135.963944474
all
Post pvalue: 0.0642935706429
Pre pvalue: 9.99900009999e-05
Both pvalue: 9.99900009999e-05
joint
Post pvalue: 0.22297770223
Pre pvalue: 9.99900009999e-05
Both pvalue: 9.99900009999e-05
separate
Post pvalue: 0.339466053395
Pre pvalue: 9.99900009999e-05
Both pvalue: 9.99900009999e-05

Bacteroides_coprocola_green
[  0   4  10  25  35  37  46  49  67  69  72  74  77  80  92 110 118 129
 153]
[   0 1030    7    5  165   44  424  262  564  697 1309 1823 1892 1822
 1273  310  167   58  393]
[ 316 2500  338   69 2500  585 2500 1639 2500 2500 2500 2500 2500 2500
 2349 2500 1486  129 2500]
[0.         0.412      0.02071006 0.07246377 0.066      0.07521368
 0.1696     0.15985357 0.2256     0.2788     0.5236     0.7292
 0.7568     0.7288     0.54193274 0.124      0.11238223 0.4496124
 0.1572    ]
Birth: 1
Death: 18
20-70: 7 11
mid: 10
pre-post-abx: 7 11
Post-abx fit test: p= 0.366633366633
Post-fixation fit test: p= 0.40959040959
Pre-fixation fit test: p= 0.000999000999001
Jorde Ryman scores
[ 7.92502018e-02  3.15377458e-03 -1.08586610e-03 -3.64878413e-04
  6.52905760e-03 -1.81581124e-04  9.37687217e-04  3.77765296e-03
  2.88519962e-02  1.21171913e-02 -1.78965502e-04 -1.76307526e-04
  1.59172250e-03  1.78008845e-02 -1.34872620e-05  2.40408484e-02
  7.46714826e-03]
All Ne: 92.6344298127
Post-fixation Ne: 138.526511983
Pre-fixation Ne: 68.7279647151
Fixation time: 25
Fixation Ne: 31.25
Effective generations per day: 4.0
Nhat: 125
[  0.  16.  40. 100. 140. 148. 184. 196. 268. 276. 288. 296. 308. 320. 368. 440. 472. 516. 612.]
All Ne: 157.365676474
Post Ne: 249.407789371
Pre Ne: 125.0
Postpre Ne: 157.365676474
all
Post pvalue: 0.0960903909609
Pre pvalue: 0.002899710029
Both pvalue: 0.001299870013
joint
Post pvalue: 0.0887911208879
Pre pvalue: 0.002499750025
Both pvalue: 0.002299770023
separate
Post pvalue: 0.0861913808619
Pre pvalue: 0.010898910109
Both pvalue: 0.003299670033

Bacteroides_coprocola_red
[  0   4  10  25  35  37  46  49  67  69  72  74  77  80  92 110 118 129
 153]
[   0  410    4    1  355   45  918  238  675  312  887 1180 1063 1112
  333  135   67   15  375]
[  72  706   91   16 1806  118 1226  337 2405  939 1519 1414 1228 1300
  486  734  314   29 1055]
[0.         0.58073654 0.04395604 0.0625     0.196567   0.38135593
 0.74877651 0.70623145 0.28066528 0.33226837 0.5839368  0.83451202
 0.86563518 0.85538462 0.68518519 0.18392371 0.2133758  0.51724138
 0.35545024]
Birth: 1
Death: 18
20-70: 4 6
mid: 5
pre-post-abx: 4 9
Post-abx fit test: p= 0.301698301698
Post-fixation fit test: p= 0.783216783217
Pre-fixation fit test: p= 0.000999000999001
Jorde Ryman scores
[ 0.08550496 -0.00264645 -0.00230399  0.03744015  0.01005257 -0.00102844
  0.00964346  0.00228706  0.02385515  0.01209594 -0.00045081 -0.00052261
  0.00048823  0.01652047 -0.00010682  0.01068712 -0.00010059]
All Ne: 84.4026887776
Post-fixation Ne: 163.558708895
Pre-fixation Ne: 37.2418604818
Fixation time: 11
Fixation Ne: 15.7142857143
Effective generations per day: 7.0
Nhat: 110
[   0.   28.   70.  175.  245.  259.  322.  343.  469.  483.  504.  518. 539.  560.  644.  770.  826.  903. 1071.]
All Ne: 174.338251171
Post Ne: 219.478854647
Pre Ne: 110.0
Postpre Ne: 174.338251171
all
Post pvalue: 0.00629937006299
Pre pvalue: 9.99900009999e-05
Both pvalue: 9.99900009999e-05
joint
Post pvalue: 0.011498850115
Pre pvalue: 9.99900009999e-05
Both pvalue: 9.99900009999e-05
separate
Post pvalue: 0.015398460154
Pre pvalue: 0.000499950005
Both pvalue: 9.99900009999e-05

Alistipes_onderdonkii
[  0   4  10  25  35  37  46  49  67  69  72  74  77  80  92 110 118 129
 153]
[ 27  37   0   6  28   4   1   1 305  72 299  40  80 110  30  52  80 193
 114]
[474 293  39 154 250 121 269  91 379  81 392  58 132 265  85 177 139 395
 262]
[0.05696203 0.12627986 0.         0.03896104 0.112      0.03305785
 0.00371747 0.01098901 0.80474934 0.88888889 0.7627551  0.68965517
 0.60606061 0.41509434 0.35294118 0.29378531 0.57553957 0.48860759
 0.4351145 ]
Birth: 0
Death: 18
20-70: 7 8
mid: 8
pre-post-abx: 7 9
Post-abx fit test: p= 0.0579420579421
Post-fixation fit test: p= 0.334665334665
Pre-fixation fit test: p= 0.000999000999001
Jorde Ryman scores
[ 0.01034511  0.01679892 -0.00137391  0.00455998  0.02635878  0.00362493
 -0.00038333  0.0390743  -0.00702909 -0.00395919 -0.00887822 -0.0071815
  0.0075534  -0.00083758 -0.00055507  0.01073106 -0.00029608 -0.0001286 ]
All Ne: 203.564834028
Post-fixation Ne: -945.103587966
Pre-fixation Ne: 116.802016826
Fixation time: 18
Fixation Ne: 18.0
Effective generations per day: 6.0
Nhat: 108
[  0.  24.  60. 150. 210. 222. 276. 294. 402. 414. 432. 444. 462. 480.
 552. 660. 708. 774. 918.]
All Ne: 135.963944474
Post Ne: 429.955744198
Pre Ne: 1359.63944474
Postpre Ne: 681.433932039
all
Post pvalue: 0.019798020198
Pre pvalue: 0.004799520048
Both pvalue: 0.000199980002
joint
Post pvalue: 0.011198880112
Pre pvalue: 0.0556944305569
Both pvalue: 0.004299570043
separate
Post pvalue: 0.026797320268
Pre pvalue: 0.025497450255
Both pvalue: 0.002699730027

Phascolactobacterium
[  0   4  10  25  35  37  46  49  67  69  72  74  77  80  92 110 118 153]
[  7 292   5  25  29  11  90  13 485 125 548 718 197 884 258 124  74  40]
[  79  508   87  255  524  154 1324  155  485  125  548  720  197  926
  270  152  182  878]
[0.08860759 0.57480315 0.05747126 0.09803922 0.05534351 0.07142857
 0.06797583 0.08387097 1.         1.         1.         0.99722222
 1.         0.95464363 0.95555556 0.81578947 0.40659341 0.04555809]
Birth: 0
Death: 17
20-70: 7 8
mid: 7
pre-post-abx: 7 9
Post-abx fit test: p= 0.000999000999001
Post-fixation fit test: p= 0.000999000999001
Pre-fixation fit test: p= 0.877122877123
Jorde Ryman scores
[ 0.09684899  0.07847317 -0.00020604  0.00167499 -0.00145907 -0.00070856
 -0.00076678  0.03242912 -0.00507141 -0.00328087 -0.00160908 -0.002166
 -0.00203923 -0.00040011 -0.00042733  0.01128831  0.01123164]
All Ne: 79.509200498
Post-fixation Ne: 1195.86791854
Pre-fixation Ne: 40.2630443209
Fixation time: 18
Fixation Ne: 13.8461538462
Effective generations per day: 8.0
Nhat: 110
[   0.   32.   80.  200.  280.  296.  368.  392.  536.  552.  576.  592.
  616.  640.  736.  880.  944. 1224.]
All Ne: 174.338251171
Post Ne: 873.761058197
Pre Ne: 347.850542619
Postpre Ne: 551.30595699
all
Post pvalue: 9.99900009999e-05
Pre pvalue: 0.002499750025
Both pvalue: 9.99900009999e-05
joint
Post pvalue: 0.002099790021
Pre pvalue: 9.99900009999e-05
Both pvalue: 9.99900009999e-05
separate
Post pvalue: 0.00199980002
Pre pvalue: 0.000799920007999
Both pvalue: 9.99900009999e-05

Eubacterium_eligens
[  0   4  10  25  35  37  46  49  67  69  72  74  77  80  92 110 118 129
 153]
[ 236  153  553   97  188  207   97  228    4   14  180 2195 1753 2302
 1273  262  921  155  615]
[2500 2500 2500 2500 2500 2500 2500 2500 2500 2500 2500 2500 2500 2500
 2500 2500 2500 2500 2500]
[0.0944 0.0612 0.2212 0.0388 0.0752 0.0828 0.0388 0.0912 0.0016 0.0056
 0.072  0.878  0.7012 0.9208 0.5092 0.1048 0.3684 0.062  0.246 ]
Birth: 0
Death: 18
20-70: 10 11
mid: 11
pre-post-abx: 7 11
Post-abx fit test: p= 0.633366633367
Post-fixation fit test: p= 0.58041958042
Pre-fixation fit test: p= 0.521478521479
Jorde Ryman scores
[ 3.03656194e-03  2.47596983e-02  1.39570239e-02  2.08324298e-03
 -6.54787993e-05  3.18541328e-03  1.26812580e-02  8.67998965e-03
  1.58907079e-03  3.47950056e-02  3.03661312e-01  2.50439387e-03
  3.47044981e-03  5.46538694e-03  1.86992650e-02  2.63783056e-02
  2.85314285e-02  7.34850962e-03]
All Ne: 35.9453029847
Post-fixation Ne: 75.7594293195
Pre-fixation Ne: 95.5093548635
Fixation time: 2
Fixation Ne: 1.81818181818
Effective generations per day: 56.0
Nhat: 101
[   0.  224.  560. 1400. 1960. 2072. 2576. 2744. 3752. 3864. 4032. 4144.
 4312. 4480. 5152. 6160. 6608. 7224. 8568.]
All Ne: 1271.51466591
Post Ne: 1600.74212439
Pre Ne: 6372.66917925
Postpre Ne: 2537.00529582
all
Post pvalue: 0.000999900009999
Pre pvalue: 0.003899610039
Both pvalue: 0.000199980002
joint
Post pvalue: 0.000299970003
Pre pvalue: 0.155384461554
Both pvalue: 0.001399860014
separate
Post pvalue: 0.001699830017
Pre pvalue: 0.182581741826
Both pvalue: 0.002599740026
