Add warfarin/pheno cov examples

nlmixr2 · May 16, 2024 · a14325e · a14325e
1 parent 6fe8960
commit a14325e
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diff --git a/inst/cov/data/phenobarbital_data.csv b/inst/cov/data/phenobarbital_data.csv
diff --git a/inst/cov/data/warfarin_data.csv b/inst/cov/data/warfarin_data.csv
diff --git a/inst/cov/pb/FisherInformation/correlationEstimatesSA.txt b/inst/cov/pb/FisherInformation/correlationEstimatesSA.txt
@@ -0,0 +1,7 @@
+V_pop,1,-0.647912,-0.435907,-0.0992874,-0.0121518,0.0317767,0.00238409
+beta_V_tAPGAR_High,-0.647912,1,0.282449,0.00797906,0.0131849,0.0204614,-0.0137715
+beta_V_tAPGAR_Low,-0.435907,0.282449,1,0.032804,0.0162185,-0.0377099,0.0183612
+k_pop,-0.0992874,0.00797906,0.032804,1,0.0223266,-0.439182,0.0875303
+omega_V,-0.0121518,0.0131849,0.0162185,0.0223266,1,-0.075066,-0.0142108
+omega_k,0.0317767,0.0204614,-0.0377099,-0.439182,-0.075066,1,-0.167853
+b,0.00238409,-0.0137715,0.0183612,0.0875303,-0.0142108,-0.167853,1
diff --git a/inst/cov/pb/FisherInformation/covarianceEstimatesSA.txt b/inst/cov/pb/FisherInformation/covarianceEstimatesSA.txt
@@ -0,0 +1,7 @@
+V_pop,0.0056467,-0.00560103,-0.00562705,-0.000379087,-3.56709e-05,0.000164807,1.51502e-06
+beta_V_tAPGAR_High,-0.00560103,0.0132346,0.00558194,4.66395e-05,5.92522e-05,0.000162465,-1.33978e-05
+beta_V_tAPGAR_Low,-0.00562705,0.00558194,0.0295107,0.000286328,0.000108837,-0.00044711,2.66741e-05
+k_pop,-0.000379087,4.66395e-05,0.000286328,0.00258163,4.43143e-05,-0.00154014,3.76102e-05
+omega_V,-3.56709e-05,5.92522e-05,0.000108837,4.43143e-05,0.00152598,-0.000202389,-4.69453e-06
+omega_k,0.000164807,0.000162465,-0.00044711,-0.00154014,-0.000202389,0.00476364,-9.79711e-05
+b,1.51502e-06,-1.33978e-05,2.66741e-05,3.76102e-05,-4.69453e-06,-9.79711e-05,7.15152e-05
diff --git a/inst/cov/pb/IndividualParameters/estimatedIndividualParameters.txt b/inst/cov/pb/IndividualParameters/estimatedIndividualParameters.txt
@@ -0,0 +1,60 @@
+id,V_SAEM,k_SAEM,V_mean,k_mean,V_mode,k_mode,V_sd,k_sd,WEIGHT,APGAR,tAPGAR
+1,1.36507,0.00450273,1.3446,0.00466268,1.36552,0.00458173,0.0990519,0.000767584,1.4,7,Med
+2,1.23866,0.00437386,1.23165,0.00460192,1.26824,0.00426925,0.0890833,0.000751667,1.5,9,High
+3,1.6821,0.00505469,1.71966,0.00511226,1.69198,0.00509029,0.126212,0.000783286,1.5,6,Med
+4,0.89023,0.00475518,0.911,0.00455246,0.907639,0.00465635,0.0645684,0.000701659,0.9,6,Med
+5,1.84085,0.00506347,1.88133,0.00495185,1.85084,0.00493041,0.140949,0.000816188,1.4,7,Med
+6,1.30114,0.00437466,1.27259,0.00460632,1.30184,0.00448675,0.0866722,0.000634497,1.2,5,Med
+7,1.04565,0.00485025,1.06903,0.00467764,1.05672,0.00483199,0.0845241,0.000679324,1,5,Med
+8,0.970299,0.00514392,0.970992,0.00514736,0.974837,0.00507549,0.0682255,0.000962446,1.2,7,Med
+9,1.19854,0.00411757,1.19733,0.00403461,1.21544,0.00409497,0.0881007,0.000443903,1.4,8,High
+10,1.3769,0.0048506,1.37805,0.00484662,1.38882,0.00483168,0.09917,0.0007317,1.4,7,Med
+11,1.80279,0.00515855,1.84577,0.0050506,1.83575,0.00489009,0.172533,0.000821175,1.2,7,Med
+12,1.36276,0.00439652,1.3975,0.0042596,1.37068,0.00437274,0.101222,0.000421236,1.3,6,Med
+13,0.91407,0.00463514,0.926068,0.00445003,0.917154,0.00467918,0.0652446,0.00072902,1.1,6,Med
+14,0.968937,0.00572103,0.99174,0.00552517,0.981756,0.00562748,0.0622939,0.000407642,1.1,7,Med
+15,1.3392,0.00505013,1.36347,0.0047548,1.37166,0.00477776,0.119671,0.000836597,1.3,7,Med
+16,1.22145,0.00405371,1.19283,0.00443368,1.20382,0.00429512,0.0741338,0.000612968,1.2,9,High
+17,1.03612,0.0045483,1.03995,0.00465647,1.04292,0.00452619,0.0535836,0.000779155,1.1,5,Med
+18,1.074,0.00638388,1.07805,0.00629808,1.08859,0.00628585,0.0839612,0.000350779,1,5,Med
+19,1.0813,0.00471885,1.07154,0.00499549,1.08935,0.00481758,0.0866937,0.000803975,1,1,Low
+20,1.07193,0.00516801,1.08486,0.00502455,1.0895,0.00495601,0.0664833,0.000811289,1.2,6,Med
+21,1.63102,0.0047654,1.62867,0.00463639,1.63167,0.00479216,0.155145,0.000623158,1.8,7,Med
+22,1.37482,0.00480672,1.39178,0.00498105,1.38735,0.00480865,0.10744,0.00089797,1.5,8,High
+23,2.72362,0.00568031,2.69069,0.00576692,2.71723,0.00557442,0.195654,0.000974405,3.1,3,Low
+24,3.53858,0.00539914,3.43387,0.00555631,3.48289,0.0054334,0.249054,0.000707746,3.2,2,Low
+25,1.06391,0.00386967,1.04797,0.0041991,1.05384,0.0041458,0.0414753,0.000593862,0.7,1,Low
+26,2.98731,0.00481891,2.95843,0.00488103,2.91446,0.00498772,0.236784,0.000828262,3.5,9,High
+27,1.354,0.00519834,1.37521,0.00507132,1.37845,0.00499655,0.127487,0.00091705,1.9,5,Med
+28,3.32997,0.00501016,3.42084,0.00492941,3.36217,0.00480582,0.373534,0.000923345,3.2,9,High
+29,0.985641,0.00469107,1.01877,0.00471696,1.01585,0.00475799,0.101668,0.000898363,1,7,Med
+30,1.90815,0.00469364,1.90892,0.00491507,1.94594,0.00472863,0.204962,0.00068543,1.8,8,High
+31,1.22709,0.00490806,1.21215,0.00511139,1.21756,0.00479711,0.115942,0.000824596,1.4,8,High
+32,4.96601,0.00507385,4.87568,0.00503065,4.94262,0.00499475,0.365989,0.000746195,3.6,9,High
+33,1.5253,0.00472151,1.50948,0.00477455,1.53975,0.00467739,0.12416,0.000946615,1.7,8,High
+34,1.54524,0.00470046,1.52716,0.00478211,1.52388,0.0048086,0.134443,0.000899913,1.7,4,Med
+35,1.80226,0.00476678,1.87218,0.00474843,1.86638,0.00458585,0.179566,0.000891753,2.5,5,Med
+36,1.41707,0.00542492,1.42152,0.00546417,1.41391,0.00558791,0.111035,0.000448293,1.5,5,Med
+37,1.21583,0.00454308,1.21562,0.00449646,1.22542,0.00464353,0.0634087,0.000652584,1.2,9,High
+38,1.42374,0.00503918,1.43182,0.00508952,1.43821,0.00500464,0.0938143,0.000409346,1.3,8,High
+39,1.88371,0.00516055,1.86076,0.00525898,1.85515,0.00524287,0.148936,0.000584956,1.9,10,High
+40,1.36948,0.00497986,1.37473,0.00493004,1.37889,0.00479692,0.120757,0.000990846,1.1,3,Low
+41,1.86093,0.00485832,1.84917,0.00476156,1.86596,0.00484356,0.118248,0.000771871,1.7,7,Med
+42,4.19461,0.00596577,4.17058,0.00588161,4.27871,0.00541521,0.286496,0.00105831,2.8,9,High
+43,0.836117,0.00480345,0.824381,0.00495039,0.837975,0.0047933,0.0755358,0.000821687,0.9,1,Low
+44,1.49596,0.00466369,1.45836,0.00466319,1.48172,0.00470082,0.114864,0.000463702,1.4,7,Med
+45,0.938179,0.00453504,0.92598,0.00473575,0.938387,0.00464707,0.0644822,0.000700612,0.8,2,Low
+46,1.10517,0.00477249,1.10879,0.00477912,1.1257,0.00479537,0.11451,0.000827035,1.1,8,High
+47,2.27986,0.00490235,2.2725,0.00487477,2.29154,0.00484686,0.234556,0.000944721,2.6,9,High
+48,0.725826,0.00338584,0.727778,0.00344076,0.709853,0.00363822,0.0439024,0.000428403,0.7,8,High
+49,1.40904,0.00452594,1.39116,0.00483219,1.41252,0.004618,0.0849743,0.000668962,1.3,8,High
+50,0.884347,0.00530195,0.882162,0.00517182,0.89538,0.00491303,0.0450933,0.00106172,1.1,6,Med
+51,1.11976,0.00435061,1.14044,0.00423379,1.12879,0.00429352,0.0737652,0.000765667,0.9,9,High
+52,0.749937,0.0055283,0.748929,0.00574792,0.741763,0.00584408,0.047788,0.000872427,0.9,7,Med
+53,1.51642,0.0045936,1.50994,0.00474449,1.53568,0.00456475,0.127226,0.00109609,1.7,8,High
+54,1.38003,0.00475195,1.38743,0.00445518,1.38124,0.00467501,0.075496,0.000667736,1.8,8,High
+55,1.56763,0.00487203,1.55777,0.00484869,1.57469,0.00486167,0.201176,0.000770133,1.1,4,Med
+56,0.690686,0.00479029,0.694776,0.00482393,0.692031,0.00474518,0.0621356,0.000859716,0.6,4,Med
+57,1.98954,0.00502514,1.99814,0.00496364,1.99014,0.00498249,0.137482,0.000736982,2.1,6,Med
+58,1.21562,0.00499815,1.20255,0.00501633,1.22259,0.00496959,0.093285,0.000741269,1.4,8,High
+59,0.96167,0.00467771,0.969286,0.00463854,0.976577,0.00460034,0.0761073,0.000866162,1.1,6,Med
diff --git a/inst/cov/pb/IndividualParameters/estimatedRandomEffects.txt b/inst/cov/pb/IndividualParameters/estimatedRandomEffects.txt
@@ -0,0 +1,60 @@
+id,eta_V_SAEM,eta_k_SAEM,eta_V_mean,eta_k_mean,eta_V_mode,eta_k_mode,eta_V_sd,eta_k_sd,WEIGHT,APGAR,tAPGAR
+1,0.0889532,-0.0732039,0.0726794,-0.043725,0.0908758,-0.0462315,0.0746714,0.178475,1.4,7,Med
+2,-0.273014,-0.101827,-0.275453,-0.0551755,-0.243606,-0.11687,0.0714567,0.163694,1.5,9,High
+3,0.298849,0.0455526,0.318751,0.0516244,0.305241,0.0590254,0.0739476,0.153573,1.5,6,Med
+4,-0.336945,-0.0140647,-0.316397,-0.064412,-0.317567,-0.0300765,0.0712033,0.153402,0.9,6,Med
+5,0.38979,0.0504285,0.408511,0.0183559,0.394979,0.0271139,0.0750348,0.160766,1.4,7,Med
+6,0.0422678,-0.10057,0.0181382,-0.0504928,0.043121,-0.0671799,0.0668564,0.139345,1.2,5,Med
+7,-0.176119,0.00559015,-0.157004,-0.0360943,-0.165489,0.00694914,0.0785078,0.145783,1,5,Med
+8,-0.252185,0.0632649,-0.25254,0.0515662,-0.246144,0.0561136,0.0697793,0.196942,1.2,7,Med
+9,-0.305943,-0.149024,-0.30385,-0.179655,-0.286133,-0.158549,0.0735623,0.112934,1.4,8,High
+10,0.0990451,0.00582259,0.0974394,-0.00158811,0.107799,0.00688479,0.0716391,0.152962,1.4,7,Med
+11,0.365531,0.0670761,0.387828,0.0382643,0.386793,0.0189021,0.0943022,0.160349,1.2,7,Med
+12,0.0878584,-0.0845335,0.111395,-0.123992,0.0946519,-0.0929202,0.0725854,0.0985337,1.3,6,Med
+13,-0.31216,-0.0390774,-0.300066,-0.088659,-0.307138,-0.0251868,0.073018,0.163204,1.1,6,Med
+14,-0.252475,0.181669,-0.230905,0.138234,-0.239071,0.159353,0.0623661,0.0748375,1.1,7,Med
+15,0.0678552,0.0442651,0.085409,-0.0244879,0.0953652,-0.00433679,0.0898102,0.175319,1.3,7,Med
+16,-0.286659,-0.172342,-0.306834,-0.0886189,-0.29574,-0.11083,0.0621496,0.138583,1.2,9,High
+17,-0.186425,-0.0593193,-0.182845,-0.0445817,-0.178636,-0.0584296,0.0523858,0.172602,1.1,5,Med
+18,-0.149229,0.292797,-0.14854,0.270389,-0.135771,0.269991,0.0779559,0.0555785,1,5,Med
+19,-0.277014,-0.0289622,-0.282805,0.0276625,-0.263025,0.00396264,0.081386,0.157847,1,1,Low
+20,-0.151623,0.0728385,-0.141106,0.0331147,-0.134942,0.0322916,0.0619082,0.160618,1.2,6,Med
+21,0.266473,-0.00868031,0.262477,-0.0432221,0.268944,-0.00132736,0.0968281,0.132539,1.8,7,Med
+22,-0.169213,-0.00859959,-0.153623,0.0214533,-0.153838,0.00210688,0.0770543,0.177591,1.5,8,High
+23,0.645646,0.161013,0.638538,0.169689,0.651005,0.149879,0.0728982,0.168566,3.1,3,Low
+24,0.908832,0.115272,0.88251,0.138346,0.899254,0.124255,0.0713464,0.129475,3.2,2,Low
+25,-0.292107,-0.217187,-0.302538,-0.143957,-0.29617,-0.146214,0.0395071,0.147234,0.7,1,Low
+26,0.605163,-0.0128711,0.600212,0.00257728,0.588449,0.0386698,0.0802233,0.170679,3.5,9,High
+27,0.079961,0.0705278,0.0935741,0.0387287,0.100304,0.0404379,0.0940524,0.183384,1.9,5,Med
+28,0.710166,0.0316529,0.742568,0.00871231,0.731351,0.00151964,0.110931,0.192855,3.2,9,High
+29,-0.239373,-0.0304589,-0.206981,-0.0340052,-0.204928,-0.00848361,0.0990519,0.181235,1,7,Med
+30,0.157033,-0.0255281,0.159462,0.0143843,0.184507,-0.0146744,0.108604,0.138613,1.8,8,High
+31,-0.283947,0.00718304,-0.293454,0.0496942,-0.284384,-0.000294747,0.0963636,0.166077,1.4,8,High
+32,1.11616,0.040031,1.10011,0.0360944,1.11666,0.0400786,0.0770605,0.150084,3.6,9,High
+33,-0.0651804,-0.0208583,-0.0729126,-0.0252667,-0.0496166,-0.0255698,0.0834029,0.204365,1.7,8,High
+34,0.213464,-0.0293972,0.198773,-0.0213208,0.200603,0.00209658,0.0898587,0.190196,1.7,4,Med
+35,0.365489,-0.0187217,0.401731,-0.027004,0.403344,-0.045333,0.0977774,0.179296,2.5,5,Med
+36,0.127942,0.129343,0.127953,0.126406,0.125699,0.152296,0.0794003,0.0845266,1.5,5,Med
+37,-0.292933,-0.057286,-0.287323,-0.0751272,-0.277955,-0.0328346,0.0517306,0.141102,1.2,9,High
+38,-0.133683,0.0530762,-0.124431,0.0556004,-0.117839,0.0420563,0.0654573,0.0812033,1.3,8,High
+39,0.146013,0.0746865,0.136538,0.085326,0.136731,0.0885594,0.0802211,0.112982,1.9,10,High
+40,-0.0407484,0.0276321,-0.0340675,0.00745074,-0.027327,-0.000334993,0.085531,0.1973,1.1,3,Low
+41,0.399999,0.00709871,0.391999,-0.0207645,0.403118,0.00934112,0.0647646,0.161564,1.7,7,Med
+42,0.946346,0.20657,0.944458,0.186499,0.972416,0.120903,0.0687624,0.187367,2.8,9,High
+43,-0.535873,-0.0126244,-0.545912,0.0173665,-0.525374,-0.00108929,0.0914706,0.16677,0.9,1,Low
+44,0.179993,-0.0254146,0.153471,-0.0335694,0.172546,-0.0205712,0.0803606,0.0997795,1.4,7,Med
+45,-0.419447,-0.066625,-0.427929,-0.0237553,-0.4122,-0.0320716,0.0695434,0.14457,0.8,2,Low
+46,-0.390733,-0.0204809,-0.383357,-0.0189974,-0.362832,-0.000657966,0.104293,0.173456,1.1,8,High
+47,0.335064,0.00285871,0.334219,-0.0019725,0.347987,0.0100219,0.104738,0.186622,2.6,9,High
+48,-0.806607,-0.351102,-0.800897,-0.340278,-0.823934,-0.276814,0.0623941,0.123585,0.7,8,High
+49,-0.144899,-0.0664602,-0.152995,-0.00251842,-0.135863,-0.0383465,0.0618932,0.138031,1.3,8,High
+50,-0.344024,0.093339,-0.347346,0.0538998,-0.331165,0.0235817,0.0511819,0.20582,1.1,6,Med
+51,-0.374539,-0.103806,-0.35195,-0.141882,-0.36009,-0.111203,0.0654728,0.184052,0.9,9,High
+52,-0.509145,0.13856,-0.511818,0.169167,-0.519384,0.19712,0.0641487,0.150612,0.9,7,Med
+53,-0.070534,-0.0530169,-0.0726886,-0.0348276,-0.0522601,-0.0499444,0.083752,0.211892,1.7,8,High
+54,-0.164461,-0.0181261,-0.155248,-0.0851636,-0.158255,-0.0260781,0.0539236,0.147044,1.8,8,High
+55,0.224624,8.13076e-05,0.214054,-0.00259102,0.233398,0.0130731,0.131793,0.162701,1.1,4,Med
+56,-0.593988,-0.00920932,-0.588808,-0.0103186,-0.588783,-0.0111799,0.089271,0.176412,0.6,4,Med
+57,0.465882,0.0402655,0.469121,0.0225516,0.467547,0.0376207,0.0704244,0.151388,2.1,6,Med
+58,-0.292143,0.0301801,-0.299679,0.0331685,-0.280267,0.0350274,0.075211,0.15113,1.4,8,High
+59,-0.260521,-0.0309933,-0.254932,-0.0510545,-0.24436,-0.0421778,0.0784758,0.185206,1.1,6,Med