Species,Time.q,current_antibiotics.q,NewTherapy.q,VEO.q,logistic.Time,logistic.current_antibiotics,logistic.NewTherapy,logistic.VEO,beta.Time,beta.current_antibiotics,beta.NewTherapy,beta.VEO,lme.Time,lme.current_antibiotics,lme.NewTherapy,lme.VEO
Actinobacteria Bifidobacterium longum,0.659417102,0.056895364,1,0.766860736,0.06291193,-1.884990227,0.068354623,-1.796785185,0.027889752,0.385738376,0.018534666,0.011444696,,,,
Actinobacteria Bifidobacterium pseudocatenulatum,0.725557378,0.009930529,1,0.061977999,0.053288485,-1.87811589,-0.017505374,5.387695585,0.03786302,0.933646926,0.034023589,0.241350957,,,,
Actinobacteria Collinsella aerofaciens,0.241294685,0.886121269,0.616415051,0.240282689,-0.134584809,-0.543210541,-2.329563652,-17.11429371,0.021076182,0.132682882,0.349955181,0.076926609,,,,
Actinobacteria Eggerthella lenta,1,0.044304795,1,0.211686848,,,,,,,,,-4.43E-05,-0.003941602,3.66E-05,0.00238925
Actinobacteria Eggerthella unclassified,1,0.005718192,0.795768929,0.085369688,-0.007180925,-2.728443162,-0.216866998,0.825915638,-0.005923349,-0.224734537,0.244113266,0.412628457,,,,
Bacteroidetes Alistipes finegoldii,1,0.003711665,0.731642193,0.059675516,-0.011209322,-9.737369955,-3.142162501,-5.516739585,0.021008301,0.797652997,0.266255383,-0.021709369,,,,
Bacteroidetes Alistipes onderdonkii,0.832561158,0.002345411,0.406430234,0.192185658,-0.006749915,-50.69416524,-4.442716932,-1.587957726,-0.010974127,0,-0.63570293,-0.629378891,,,,
Bacteroidetes Bacteroides caccae,0.552782932,0.003711665,0.497904488,0.101951259,0.13858698,-13.80159314,13.26032122,10.58023268,-0.028720925,-0.639362813,0.25659766,0.545865026,,,,
Bacteroidetes Bacteroides dorei,0.442714757,0.00254143,0.664085443,0.026559412,-0.173970889,-2.263041286,0.041562009,-6.919202851,-0.016733863,-1.871398479,0.512921132,1.506663921,,,,
Bacteroidetes Bacteroides fragilis,1,0.013418312,0.219986288,0.211686848,-0.021846462,-2.585609919,15.74704747,1.574767473,-0.001518153,-1.073440856,0.561291886,0.422592128,,,,
Bacteroidetes Bacteroides ovatus,0.01194828,0.008289668,1,0.085369688,-0.039615877,-5.449657047,0.133000862,-6.778482921,0.049987626,-1.17511506,0.345229301,-0.11605172,,,,
Bacteroidetes Bacteroides stercoris,1,0.223472567,1,0.061977999,0.017546666,-2.459804231,-0.37749989,-5.190796779,0.011514461,-1.576705609,-0.238062416,-0.404605282,,,,
Bacteroidetes Bacteroides thetaiotaomicron,0.320889363,0.001710658,0.111145439,0.237058204,0.070768439,-56.41465428,3.069279986,-36.50066765,-0.046139359,-1.006687661,-0.223628621,0.199926264,,,,
Bacteroidetes Bacteroides uniformis,0.15348096,0.051621252,1,0.061977999,0.031329932,-4.528138536,1.441897357,-5.752741779,0.042424381,0.06975319,0.194073334,-0.014455416,,,,
Bacteroidetes Bacteroides vulgatus,0.691774875,0.327891039,1,0.059675516,-0.149790744,-1.907106585,0.274021551,-5.544990244,-0.012482609,-0.744934352,0.107740763,0.545260312,,,,
Bacteroidetes Bacteroides xylanisolvens,0.442714757,0.028319088,0.993047231,0.153688758,0.226899977,-4.333701367,-1.083708077,-5.894453556,0.019828273,0.132892428,0.329285085,0.445015729,,,,
Bacteroidetes Parabacteroides distasonis,0.96367705,0.022881361,0.731642193,0.336210106,-0.102577194,-5.922403373,2.962029448,-3.11266429,-0.003675127,-0.189190553,0.319643487,0.020144749,,,,
Bacteroidetes Parabacteroides unclassified,0.509874654,0.378453987,1,0.085369688,0.012461433,-1.14705425,-0.455111013,0.052934158,0.053200476,-0.424734638,-0.24895636,-0.825181236,,,,
Firmicutes Anaerostipes hadrus,0.61620826,0.035962985,0.08704707,0.658128397,-0.051679304,-2.866843867,-1.355110003,0.097036956,-0.027575464,0.266891594,-0.20813389,0.282360208,,,,
Firmicutes Anaerotruncus colihominis,0.241294685,0.018833268,1,0.232345555,,,,,,,,,0.000605641,-0.011586162,-0.000499856,0.006225919
Firmicutes Clostridiales bacterium 1 7 47FAA,0.988809495,0.022881361,1,0.6251155,-0.036970038,-2.325016854,-0.390901477,-0.752797154,-0.010478035,-0.11141512,0.014980644,-0.021894685,,,,
Firmicutes Clostridium asparagiforme,1,0.049161899,0.168933738,0.098620094,-0.006776171,-2.189633958,-1.418681915,-1.091799036,0.019735991,-0.033363957,0.141819816,0.321523717,,,,
Firmicutes Clostridium bartlettii,0.538919742,9.19E-05,0.853810549,0.243468018,0.027062698,-3.203382682,-0.67959853,0.83322236,0.036132818,0.048105528,0.021553708,0.190348658,,,,
Firmicutes Clostridium bolteae,1,9.19E-05,0.497904488,0.403524009,-0.018182718,-3.000552036,-0.235395147,-0.000159408,0.004697327,0.749523295,0.288882607,0.229102436,,,,
Firmicutes Clostridium citroniae,0.538919742,0.035962985,0.993047231,0.749369721,-0.083894757,-1.899581966,0.071131211,-0.214255588,0.00722268,0.407064081,-0.203734784,0.177085268,,,,
Firmicutes Clostridium clostridioforme,1,0.012126275,0.406430234,0.240282689,0.006134421,-3.805053465,-1.808798453,-1.343214913,0.003497758,-0.036751406,-0.130114285,-0.222001926,,,,
Firmicutes Clostridium hathewayi,1,0.000298274,0.715568818,0.266293019,0.02024684,-3.211538814,-0.255008123,1.040130537,-0.008880229,0.03685575,-0.254690447,-0.089614374,,,,
Firmicutes Clostridium nexile,0.008912371,9.19E-05,1,0.000187121,-0.077834847,-2.57605723,-0.159407043,2.266286764,-0.035073005,-0.532125276,0.156738535,0.603940181,,,,
Firmicutes Clostridium ramosum,0.607602223,0.005013256,0.08704707,0.033444036,-0.062256131,-4.317856804,1.107959127,3.833437814,-0.003559555,0.104902461,0.225325303,0.131890171,,,,
Firmicutes Clostridium scindens,1,0.755545783,0.993047231,0.6251155,,,,,,,,,4.96E-05,-0.000840473,-0.001258898,0.001511392
Firmicutes Clostridium symbiosum,0.15348096,5.73E-05,0.000378688,0.473990529,-0.059134351,-5.309989173,0.14733291,0.513213254,-0.063986635,0.24871216,-0.192447646,0.317386334,,,,
Firmicutes Coprobacillus unclassified,0.691774875,0.157943033,1,0.082579995,-0.08661115,-1.905321619,-0.497315903,1.560239081,-0.007425639,-0.043532607,0.061238668,0.451443296,,,,
Firmicutes Dialister invisus,0.27614676,0.007783213,0.117979733,0.237058204,0.14269678,-7921.943667,7905.065182,-2.007370026,0.030965811,-0.001562572,0.064365893,-0.234356139,,,,
Firmicutes Dorea formicigenerans,1,0.128543388,0.664732282,0.018908895,0.047084441,-1.830351327,1027.155836,-1029.491895,-0.020675282,-1.161205493,0.141017019,0.793256887,,,,
Firmicutes Dorea longicatena,1,0.000535733,0.08704707,0.061977999,0.035918646,-8874.762009,8812.778039,-8815.033265,0.009990544,0.474581104,0.219507266,0.192777441,,,,
Firmicutes Dorea unclassified,0.988809495,0.853648345,1,0.825322319,0.042992336,0.037151215,-0.043257555,0.214540515,-0.016634475,-0.229291683,0.051519747,0.150654216,,,,
Firmicutes Erysipelotrichaceae bacterium 6 1 45,0.988809495,0.792660732,0.795768929,0.749369721,,,,,,,,,7.13E-05,-0.000686493,-0.001684729,-0.000894331
Firmicutes Eubacterium eligens,0.526642566,0.016982423,1,0.508674285,0.122445028,-4.586637653,-0.15371094,0.95384104,0.02388527,-0.018755286,0.218259711,0.189787748,,,,
Firmicutes Eubacterium hallii,0.832561158,0.000127205,0.764827626,0.50541889,0.10696286,-7.860559589,-1.523942078,-2.83174289,0.00016048,1.043947248,-0.162438762,-0.077621676,,,,
Firmicutes Eubacterium rectale,0.602966388,0.001922615,1,0.6251155,0.151061559,-6.001277886,-0.866631295,3.468733074,0.001025684,0.104100687,-0.171512162,-0.04393745,,,,
Firmicutes Faecalibacterium prausnitzii,0.602966388,0.043893665,0.866772933,0.101951259,0.163263165,-2.497329636,-1.818038455,-2.142263242,-0.01098044,-0.539486656,0.219182798,0.456888456,,,,
Firmicutes Flavonifractor plautii,0.988809495,0.000871694,0.993047231,0.235181334,0.063599952,-2.432559335,0.116322258,0.785268222,0.002176387,-0.652478147,-0.331262169,0.502797499,,,,
Firmicutes Lachnospiraceae bacterium 1 1 57FAA,0.666499934,0.534241335,1,0.97970402,0.051673687,-0.925776498,0.193644155,-0.178354871,0.038787283,0.263179842,0.022884937,0.022226688,,,,
Firmicutes Lachnospiraceae bacterium 2 1 58FAA,1,0.224157398,1,0.852582796,0.005101763,-0.882620918,0.316390116,0.41049882,-0.012225231,0.588342756,-0.181335108,0.044988015,,,,
Firmicutes Lachnospiraceae bacterium 3 1 46FAA,0.241294685,0.002168985,0.000232101,0.000120171,-0.032471539,-2.917613237,-0.634477081,-1.361885076,0.010287252,-0.896982704,0.157608379,-0.085713934,,,,
Firmicutes Lachnospiraceae bacterium 3 1 57FAA CT1,1,0.122944265,1,0.766860736,0.014850597,-2.164076214,0.073291686,-0.638345199,0.019034517,-0.570323771,0.195648004,0.115213209,,,,
Firmicutes Lachnospiraceae bacterium 5 1 57FAA,0.526642566,0.337577639,0.664732282,0.825322319,0.072124613,-1.268522449,-0.989499904,0.334280005,-0.040096528,0.20697379,-0.272602489,-0.132798699,,,,
Firmicutes Lachnospiraceae bacterium 5 1 63FAA,0.47520363,0.003711665,1,0.280037503,-0.149806201,-2.508912427,-0.440026543,-0.314151758,0.024415494,-0.403796556,0.051441793,0.378186978,,,,
Firmicutes Lachnospiraceae bacterium 7 1 58FAA,0.526642566,0.009981604,1,0.551308964,,,,,,,,,-0.000357869,-0.012123821,-0.001821554,-0.003939975
Firmicutes Oscillibacter unclassified,1,0.000760658,0.731642193,0.082579995,0.035625225,-4.756490754,0.071906674,-1.216241637,-0.006878785,-1.05218277,-0.124372299,0.466698892,,,,
Firmicutes Peptostreptococcaceae noname unclassified,0.15348096,0.211722377,0.731642193,0.101951259,0.1339676,-0.129235002,-0.184045974,-1.040085631,-0.000120353,0.736539275,0.298317018,-0.021675012,,,,
Firmicutes Roseburia hominis,0.241294685,0.002619979,0.08704707,0.061977999,0.170039247,-4.001889406,-2.009145439,-1.591658842,0.011943753,-0.010276282,-0.144293906,0.314246124,,,,
Firmicutes Roseburia intestinalis,0.241294685,0.008289668,0.866772933,0.473990529,0.146880229,-2.591544031,-0.614245638,0.782830561,0.014353164,-0.513367201,0.191349492,0.198672853,,,,
Firmicutes Roseburia inulinivorans,0.241294685,0.000343402,1,0.14637542,0.149063849,-4.579783304,-0.321166446,-0.073103878,0.025729691,-0.624098148,0.048681381,0.392775831,,,,
Firmicutes Roseburia unclassified,0.988809495,0.907158842,1,0.658128397,-0.03810199,-0.241800591,-0.042809031,-0.518469504,-0.01405093,-0.186558544,0.083460539,-0.227778857,,,,
Firmicutes Ruminococcus gnavus,0.15348096,0.000900945,1,0.6251155,-0.248485989,-5.08417783,-0.299678149,0.156954045,-0.003797176,0.150882387,0.052031791,0.18390651,,,,
Firmicutes Ruminococcus lactaris,0.832561158,0.286634957,0.715568818,0.9648419,-0.072869842,1.492410124,-18.01093392,0.311129431,-0.02721251,-0.574487326,-0.537099441,0.043383424,,,,
Firmicutes Ruminococcus obeum,0.988809495,0.038320522,1,0.151167075,0.044919607,-2.638925506,-1.077048186,-2.277032074,0.012673447,-0.008854969,0.026931635,-0.012152291,,,,
Firmicutes Ruminococcus sp 5 1 39BFAA,1,0.373529254,1,0.766860736,-0.03988834,-1.309648078,-0.270963877,0.024229766,0.003111994,0.249328868,0.204225447,0.248363965,,,,
Firmicutes Ruminococcus torques,0.979871424,0.000280981,0.866772933,0.658128397,0.051385817,-4.055280298,-0.729634861,-1.16160095,-0.012231493,-0.411686121,0.192874711,-0.057409962,,,,
Firmicutes Streptococcus parasanguinis,1,0.573282507,0.715568818,0.203334301,0.012228505,0.752901939,0.559079806,0.763710519,0.00702637,0.063088715,0.23174744,0.290298019,,,,
Firmicutes Streptococcus salivarius,0.934950435,0.577138758,0.930969941,0.1323291,0.047430453,-0.185519188,-0.158959523,0.661850804,0.014030837,0.243289474,0.17479885,0.311845035,,,,
Firmicutes Streptococcus thermophilus,0.552782932,0.286634957,0.993047231,0.358902681,-0.072468782,0.911221179,0.015120356,0.3147631,0.027353548,0.306053678,-0.184532271,0.2980672,,,,
Firmicutes Subdoligranulum unclassified,1,0.007730343,1,0.825322319,-0.049935072,-3.816363697,-0.551950843,-0.61872855,0.002461065,-0.050910355,-0.041054416,-0.146241002,,,,
Firmicutes Veillonella atypica,0.241294685,0.002499901,1,0.093583916,-0.135526216,-3.205619543,0.098569945,1.756083981,0.003133795,0.226599109,-0.118915832,0.100409544,,,,
Firmicutes Veillonella dispar,0.442714757,0.014004628,1,0.053632084,-0.094614027,-2.020049586,0.307308078,1.776625659,-0.022335074,0.436854092,0.010431233,0.057117338,,,,
Firmicutes Veillonella parvula,0.509874654,0.001710658,1,0.093583916,-0.100447507,-2.080679933,-0.158755754,1.543534833,-0.013289624,0.786655086,-0.066113896,-0.030098161,,,,
Firmicutes Veillonella unclassified,0.602966388,0.007783213,0.866772933,0.033444036,0.020045198,-2.623484852,0.371354066,1.722952979,-0.035931678,0.209582143,0.194183955,0.377468963,,,,
Proteobacteria Bilophila unclassified,1,0.002168985,1,1,0.055253847,-86.70852656,-0.482227221,30.63993392,-0.051362834,0.351827261,0.489411284,0.066442774,,,,
Proteobacteria Bilophila wadsworthia,0.662848492,0.096806396,0.731642193,0.102297065,-0.077416051,-2.706151803,0.327449917,-1.493109536,-0.020774207,0.211010737,0.467436491,-0.640719127,,,,
Proteobacteria Burkholderiales bacterium 1 1 47,0.15348096,0.194540094,0.08704707,1,-0.000752667,2.231645043,-16.64044876,0.179093254,0.007960506,0.056759447,0.07448337,0.268806762,,,,
Proteobacteria Escherichia coli,1,0.189614562,1,0.828177005,-0.007502216,-0.495050793,0.000718316,-0.032289115,-0.00557818,0.481761017,-0.083071438,0.117100616,,,,
Proteobacteria Escherichia unclassified,1,0.184123667,1,0.886319466,-0.015686082,0.406265284,0.183517592,0.023947086,0.008776656,0.563920306,0.07531669,0.124710167,,,,
Proteobacteria Haemophilus parainfluenzae,1,0.064829275,0.374778864,0.014016701,0.022303841,-1.803524691,0.916054184,2.549043721,-0.008504048,0.352118858,0.306057351,0.18228618,,,,
Proteobacteria Parasutterella excrementihominis,1,1,0.000232101,0.061977999,-0.021091736,-1.195000007,-2.156695704,0.191624183,0.015889124,-0.262334923,-0.076926872,0.964125812,,,,
Verrucomicrobia Akkermansia muciniphila,1,0.573282507,0.73436934,0.061977999,0.003216596,-0.534773963,-0.461162233,-0.028898524,0.004505453,-0.368150824,-0.348275459,-0.712782362,,,,
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"If the taxa has less than 10 zeros or the maximum abundance is too small, the ZIBR test may not be accurate so we used the results of the linear mixed effect model as suggested.",,,,,,,,,,,,,,,,