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+8,9,.,11.4,1,50,0,27 +8,12,.,11,1,50,0,27 +8,24,.,9.1,1,50,0,27 +8,24,.,33,2,50,0,27 +8,36,.,8.2,1,50,0,27 +8,36,.,22,2,50,0,27 +8,48,.,5.9,1,50,0,27 +8,48,.,16,2,50,0,27 +8,72,.,3.6,1,50,0,27 +8,72,.,18,2,50,0,27 +8,96,.,1.7,1,50,0,27 +8,96,.,32,2,50,0,27 +8,120,.,1.1,1,50,0,27 +8,120,.,30,2,50,0,27 +8,144,.,45,2,50,0,27 +9,0,105,.,.,70,1,28 +9,0,.,92,2,70,1,28 +9,24,.,8.6,1,70,1,28 +9,24,.,39,2,70,1,28 +9,36,.,8,1,70,1,28 +9,36,.,22,2,70,1,28 +9,48,.,6,1,70,1,28 +9,48,.,17,2,70,1,28 +9,72,.,4.4,1,70,1,28 +9,72,.,17,2,70,1,28 +9,96,.,3.6,1,70,1,28 +9,96,.,22,2,70,1,28 +9,120,.,2.8,1,70,1,28 +9,120,.,25,2,70,1,28 +9,144,.,33,2,70,1,28 +10,0,100,.,.,66.7,1,50 +10,0.5,.,0.01,1,66.7,1,50 +10,1,.,1.9,1,66.7,1,50 +10,2,.,3.3,1,66.7,1,50 +10,3,.,6.6,1,66.7,1,50 +10,6,.,9.1,1,66.7,1,50 +10,9,.,10.8,1,66.7,1,50 +10,12,.,8.6,1,66.7,1,50 +10,24,.,5.6,1,66.7,1,50 +10,24,.,44,2,66.7,1,50 +10,36,.,4,1,66.7,1,50 +10,36,.,27,2,66.7,1,50 +10,48,.,2.7,1,66.7,1,50 +10,48,.,28,2,66.7,1,50 +10,72,.,0.8,1,66.7,1,50 +10,72,.,31,2,66.7,1,50 +10,96,.,60,2,66.7,1,50 +10,120,.,65,2,66.7,1,50 +10,144,.,71,2,66.7,1,50 +11,0,123,.,.,82,1,31 +11,0,.,99,2,82,1,31 +11,1.5,.,11.4,1,82,1,31 +11,3,.,15.4,1,82,1,31 +11,6,.,17.5,1,82,1,31 +11,12,.,14,1,82,1,31 +11,24,.,9,1,82,1,31 +11,24,.,37,2,82,1,31 +11,36,.,8.9,1,82,1,31 +11,36,.,24,2,82,1,31 +11,48,.,6.6,1,82,1,31 +11,48,.,14,2,82,1,31 +11,72,.,4.2,1,82,1,31 +11,72,.,11,2,82,1,31 +11,96,.,3.6,1,82,1,31 +11,96,.,14,2,82,1,31 +11,120,.,2.6,1,82,1,31 +11,120,.,23,2,82,1,31 +11,144,.,33,2,82,1,31 +12,0,113,.,.,75.3,1,32 +12,0,.,95,2,75.3,1,32 +12,1.5,.,0.6,1,75.3,1,32 +12,3,.,2.8,1,75.3,1,32 +12,6,.,13.8,1,75.3,1,32 +12,9,.,15,1,75.3,1,32 +12,24,.,10.5,1,75.3,1,32 +12,24,.,25,2,75.3,1,32 +12,36,.,9.1,1,75.3,1,32 +12,36,.,15,2,75.3,1,32 +12,48,.,6.6,1,75.3,1,32 +12,48,.,11,2,75.3,1,32 +12,72,.,4.9,1,75.3,1,32 +12,96,.,2.4,1,75.3,1,32 +12,120,.,1.9,1,75.3,1,32 +13,0,113,.,.,75.3,1,63 +13,0,.,97,2,75.3,1,63 +13,1.5,.,3.6,1,75.3,1,63 +13,3,.,12.9,1,75.3,1,63 +13,6,.,12.9,1,75.3,1,63 +13,9,.,10.2,1,75.3,1,63 +13,24,.,6.4,1,75.3,1,63 +13,24,.,41,2,75.3,1,63 +13,36,.,6.9,1,75.3,1,63 +13,36,.,23,2,75.3,1,63 +13,48,.,4.5,1,75.3,1,63 +13,48,.,16,2,75.3,1,63 +13,72,.,3.2,1,75.3,1,63 +13,72,.,14,2,75.3,1,63 +13,96,.,2.4,1,75.3,1,63 +13,96,.,18,2,75.3,1,63 +13,120,.,1.3,1,75.3,1,63 +13,120,.,22,2,75.3,1,63 +13,144,.,35,2,75.3,1,63 +14,0,75,.,.,50,0,36 +14,0,.,95,2,50,0,36 +14,0.5,.,0.02,1,50,0,36 +14,1,.,2.7,1,50,0,36 +14,2,.,11.6,1,50,0,36 +14,3,.,11.6,1,50,0,36 +14,6,.,11.3,1,50,0,36 +14,9,.,9.7,1,50,0,36 +14,24,.,6.5,1,50,0,36 +14,24,.,32,2,50,0,36 +14,36,.,5.2,1,50,0,36 +14,36,.,22,2,50,0,36 +14,48,.,3.6,1,50,0,36 +14,48,.,21,2,50,0,36 +14,72,.,2.4,1,50,0,36 +14,72,.,28,2,50,0,36 +14,96,.,0.9,1,50,0,36 +14,96,.,38,2,50,0,36 +14,120,.,46,2,50,0,36 +14,144,.,65,2,50,0,36 +15,0,85,.,.,56.7,0,27 +15,0,.,98,2,56.7,0,27 +15,1,.,6.6,1,56.7,0,27 +15,3,.,11.9,1,56.7,0,27 +15,6,.,11.7,1,56.7,0,27 +15,9,.,12.2,1,56.7,0,27 +15,24,.,8.1,1,56.7,0,27 +15,24,.,43,2,56.7,0,27 +15,36,.,7.4,1,56.7,0,27 +15,36,.,26,2,56.7,0,27 +15,48,.,6.8,1,56.7,0,27 +15,48,.,15,2,56.7,0,27 +15,72,.,5.3,1,56.7,0,27 +15,72,.,13,2,56.7,0,27 +15,96,.,3,1,56.7,0,27 +15,96,.,21,2,56.7,0,27 +15,120,.,2,1,56.7,0,27 +15,120,.,28,2,56.7,0,27 +15,144,.,39,2,56.7,0,27 +16,0,87,.,.,58,1,22 +16,0,.,99,2,58,1,22 +16,24,.,10.4,1,58,1,22 +16,24,.,42,2,58,1,22 +16,36,.,8.9,1,58,1,22 +16,36,.,32,2,58,1,22 +16,48,.,7,1,58,1,22 +16,48,.,26,2,58,1,22 +16,72,.,4.4,1,58,1,22 +16,72,.,31,2,58,1,22 +16,96,.,3.2,1,58,1,22 +16,96,.,33,2,58,1,22 +16,120,.,2.4,1,58,1,22 +16,120,.,54,2,58,1,22 +17,0,117,.,.,78,1,28 +17,0,.,97,2,78,1,28 +17,24,.,7.6,1,78,1,28 +17,24,.,35,2,78,1,28 +17,36,.,6.4,1,78,1,28 +17,36,.,23,2,78,1,28 +17,48,.,6,1,78,1,28 +17,48,.,17,2,78,1,28 +17,72,.,4,1,78,1,28 +17,72,.,18,2,78,1,28 +17,96,.,3.1,1,78,1,28 +17,96,.,18,2,78,1,28 +17,120,.,2,1,78,1,28 +17,120,.,21,2,78,1,28 +18,0,112,.,.,74.7,1,31 +18,0,.,98,2,74.7,1,31 +18,24,.,7.6,1,74.7,1,31 +18,24,.,32,2,74.7,1,31 +18,36,.,6.6,1,74.7,1,31 +18,36,.,20,2,74.7,1,31 +18,48,.,5.4,1,74.7,1,31 +18,48,.,18,2,74.7,1,31 +18,72,.,3.4,1,74.7,1,31 +18,72,.,18,2,74.7,1,31 +18,96,.,1.2,1,74.7,1,31 +18,96,.,19,2,74.7,1,31 +18,120,.,0.9,1,74.7,1,31 +18,120,.,29,2,74.7,1,31 +19,0,95.5,.,.,63.7,1,22 +19,0,.,97,2,63.7,1,22 +19,24,.,6.6,1,63.7,1,22 +19,24,.,33,2,63.7,1,22 +19,36,.,5.3,1,63.7,1,22 +19,36,.,28,2,63.7,1,22 +19,48,.,3.6,1,63.7,1,22 +19,48,.,18,2,63.7,1,22 +19,72,.,2.7,1,63.7,1,22 +19,72,.,18,2,63.7,1,22 +19,96,.,1.4,1,63.7,1,22 +19,96,.,17,2,63.7,1,22 +19,120,.,1.1,1,63.7,1,22 +19,120,.,26,2,63.7,1,22 +20,0,88.5,.,.,59,1,22 +20,0,.,96,2,59,1,22 +20,24,.,9.6,1,59,1,22 +20,24,.,41,2,59,1,22 +20,36,.,8,1,59,1,22 +20,36,.,30,2,59,1,22 +20,48,.,6.6,1,59,1,22 +20,48,.,22,2,59,1,22 +20,72,.,5.6,1,59,1,22 +20,72,.,23,2,59,1,22 +20,96,.,3.5,1,59,1,22 +20,96,.,23,2,59,1,22 +20,120,.,2.3,1,59,1,22 +20,120,.,35,2,59,1,22 +21,0,93,.,.,62,1,27 +21,0,.,98,2,62,1,27 +21,24,.,7.3,1,62,1,27 +21,24,.,46,2,62,1,27 +21,36,.,6.1,1,62,1,27 +21,36,.,27,2,62,1,27 +21,48,.,4.3,1,62,1,27 +21,48,.,22,2,62,1,27 +21,72,.,3.2,1,62,1,27 +21,72,.,36,2,62,1,27 +21,96,.,2.3,1,62,1,27 +21,96,.,40,2,62,1,27 +21,120,.,1.9,1,62,1,27 +21,120,.,44,2,62,1,27 +22,0,87,.,.,58,1,22 +22,0,.,97,2,58,1,22 +22,24,.,8.9,1,58,1,22 +22,24,.,35,2,58,1,22 +22,36,.,8.4,1,58,1,22 +22,36,.,27,2,58,1,22 +22,48,.,8,1,58,1,22 +22,48,.,23,2,58,1,22 +22,72,.,4.4,1,58,1,22 +22,72,.,27,2,58,1,22 +22,96,.,3.2,1,58,1,22 +22,96,.,43,2,58,1,22 +22,120,.,1.7,1,58,1,22 +22,120,.,43,2,58,1,22 +23,0,110,.,.,73.3,1,22 +23,0,.,98,2,73.3,1,22 +23,24,.,9.8,1,73.3,1,22 +23,24,.,34,2,73.3,1,22 +23,36,.,8.4,1,73.3,1,22 +23,36,.,24,2,73.3,1,22 +23,48,.,6.6,1,73.3,1,22 +23,48,.,15,2,73.3,1,22 +23,72,.,4.8,1,73.3,1,22 +23,72,.,15,2,73.3,1,22 +23,96,.,3.2,1,73.3,1,22 +23,96,.,19,2,73.3,1,22 +23,120,.,2.4,1,73.3,1,22 +23,120,.,19,2,73.3,1,22 +24,0,115,.,.,76.7,1,35 +24,0,.,95,2,76.7,1,35 +24,24,.,8.2,1,76.7,1,35 +24,24,.,37,2,76.7,1,35 +24,36,.,7.5,1,76.7,1,35 +24,36,.,20,2,76.7,1,35 +24,48,.,6.8,1,76.7,1,35 +24,48,.,20,2,76.7,1,35 +24,72,.,5.5,1,76.7,1,35 +24,72,.,26,2,76.7,1,35 +24,96,.,4.5,1,76.7,1,35 +24,96,.,28,2,76.7,1,35 +24,120,.,3.7,1,76.7,1,35 +24,120,.,50,2,76.7,1,35 +25,0,112,.,.,74.7,1,23 +25,0,.,99,2,74.7,1,23 +25,24,.,11,1,74.7,1,23 +25,24,.,32,2,74.7,1,23 +25,36,.,10,1,74.7,1,23 +25,36,.,20,2,74.7,1,23 +25,48,.,8.2,1,74.7,1,23 +25,48,.,17,2,74.7,1,23 +25,72,.,6,1,74.7,1,23 +25,72,.,19,2,74.7,1,23 +25,96,.,3.7,1,74.7,1,23 +25,96,.,21,2,74.7,1,23 +25,120,.,2.6,1,74.7,1,23 +25,120,.,30,2,74.7,1,23 +26,0,120,.,.,80,1,23 +26,0,.,99,2,80,1,23 +26,24,.,10,1,80,1,23 +26,24,.,41,2,80,1,23 +26,36,.,9,1,80,1,23 +26,36,.,28,2,80,1,23 +26,48,.,7.3,1,80,1,23 +26,48,.,19,2,80,1,23 +26,72,.,5.2,1,80,1,23 +26,72,.,17,2,80,1,23 +26,96,.,3.7,1,80,1,23 +26,96,.,17,2,80,1,23 +26,120,.,2.7,1,80,1,23 +26,120,.,24,2,80,1,23 +27,0,120,.,.,80,1,22 +27,0,.,99,2,80,1,22 +27,24,.,11.8,1,80,1,22 +27,24,.,32,2,80,1,22 +27,36,.,9.2,1,80,1,22 +27,36,.,21,2,80,1,22 +27,48,.,7.7,1,80,1,22 +27,48,.,19,2,80,1,22 +27,72,.,4.9,1,80,1,22 +27,72,.,22,2,80,1,22 +27,96,.,3.4,1,80,1,22 +27,96,.,33,2,80,1,22 +27,120,.,2.7,1,80,1,22 +27,120,.,46,2,80,1,22 +28,0,120,.,.,80,1,22 +28,0,.,99,2,80,1,22 +28,24,.,10.1,1,80,1,22 +28,24,.,39,2,80,1,22 +28,36,.,8,1,80,1,22 +28,36,.,25,2,80,1,22 +28,48,.,6,1,80,1,22 +28,48,.,16,2,80,1,22 +28,72,.,4.9,1,80,1,22 +28,72,.,14,2,80,1,22 +28,96,.,3.4,1,80,1,22 +28,96,.,15,2,80,1,22 +28,120,.,2,1,80,1,22 +28,120,.,20,2,80,1,22 +29,0,153,.,.,102,1,22 +29,0,.,95,2,102,1,22 +29,24,.,8.3,1,102,1,22 +29,24,.,35,2,102,1,22 +29,36,.,7,1,102,1,22 +29,36,.,21,2,102,1,22 +29,48,.,5.6,1,102,1,22 +29,48,.,18,2,102,1,22 +29,72,.,4.1,1,102,1,22 +29,72,.,20,2,102,1,22 +29,96,.,3.1,1,102,1,22 +29,96,.,29,2,102,1,22 +29,120,.,2.2,1,102,1,22 +29,120,.,41,2,102,1,22 +30,0,105,.,.,70,1,23 +30,0,.,99,2,70,1,23 +30,24,.,9.9,1,70,1,23 +30,24,.,45,2,70,1,23 +30,36,.,7.5,1,70,1,23 +30,36,.,24,2,70,1,23 +30,48,.,6.5,1,70,1,23 +30,48,.,23,2,70,1,23 +30,72,.,4.1,1,70,1,23 +30,72,.,26,2,70,1,23 +30,96,.,2.9,1,70,1,23 +30,96,.,28,2,70,1,23 +30,120,.,2.3,1,70,1,23 +30,120,.,39,2,70,1,23 +31,0,125,.,.,83.3,1,24 +31,0,.,98,2,83.3,1,24 +31,24,.,9.5,1,83.3,1,24 +31,24,.,45,2,83.3,1,24 +31,36,.,7.8,1,83.3,1,24 +31,36,.,30,2,83.3,1,24 +31,48,.,6.4,1,83.3,1,24 +31,48,.,24,2,83.3,1,24 +31,72,.,4.5,1,83.3,1,24 +31,72,.,22,2,83.3,1,24 +31,96,.,3.4,1,83.3,1,24 +31,96,.,28,2,83.3,1,24 +31,120,.,2.5,1,83.3,1,24 +31,120,.,42,2,83.3,1,24 +32,0,93,.,.,62,1,21 +32,0,.,99,2,62,1,21 +32,24,.,8.9,1,62,1,21 +32,24,.,36,2,62,1,21 +32,36,.,7.7,1,62,1,21 +32,36,.,27,2,62,1,21 +32,48,.,6.9,1,62,1,21 +32,48,.,24,2,62,1,21 +32,72,.,4.4,1,62,1,21 +32,72,.,23,2,62,1,21 +32,96,.,3.5,1,62,1,21 +32,96,.,20,2,62,1,21 +32,120,.,2.5,1,62,1,21 +32,120,.,22,2,62,1,21 diff --git a/inst/cov/pb/FisherInformation/correlationEstimatesSA.txt b/inst/cov/pb/FisherInformation/correlationEstimatesSA.txt new file mode 100644 index 0000000..7f896a8 --- /dev/null +++ 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 new file mode 100644 index 0000000..4f22ecd --- /dev/null +++ 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 new file mode 100644 index 0000000..7aac184 --- /dev/null +++ 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 new file mode 100644 index 0000000..40f2657 --- /dev/null +++ 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 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+42,16.674542 +43,8.225448 +44,14.895918 +45,15.375531 +46,7.028963 +47,7.261535 +48,44.843945 +49,17.537611 +50,25.021518 +51,22.063701 +52,23.993910 +53,13.732008 +54,21.691504 +55,6.477952 +56,8.382310 +57,12.412103 +58,17.242933 +59,17.575928 diff --git a/inst/cov/pb/LogLikelihood/logLikelihood.txt b/inst/cov/pb/LogLikelihood/logLikelihood.txt new file mode 100644 index 0000000..236ee12 --- /dev/null +++ b/inst/cov/pb/LogLikelihood/logLikelihood.txt @@ -0,0 +1,6 @@ +criteria,importanceSampling +OFV,971.427906 +AIC,985.427906 +BIC,999.970668 +BICc,1002.868331 +standardError,0.069867 diff --git a/inst/cov/pb/Tests/correlationIndividualParametersCovariates.txt b/inst/cov/pb/Tests/correlationIndividualParametersCovariates.txt new file mode 100644 index 0000000..38b7efe --- /dev/null +++ b/inst/cov/pb/Tests/correlationIndividualParametersCovariates.txt @@ -0,0 +1,3 @@ +parameter,covariate,statistics,p-value,test +V,beta_V_tAPGAR_High,2.14297,0.0364754,t-Test +V,beta_V_tAPGAR_Low,0.621568,0.536748,t-Test diff --git a/inst/cov/pb/Tests/correlationRandomEffects.txt b/inst/cov/pb/Tests/correlationRandomEffects.txt new file mode 100644 index 0000000..29cdacb --- /dev/null +++ b/inst/cov/pb/Tests/correlationRandomEffects.txt @@ -0,0 +1,2 @@ +eta1,eta2,coeff,statistics,p-value +eta_V,eta_k,0,1.90179,0.0621694 diff --git a/inst/cov/pb/Tests/correlationRandomEffectsCovariates.txt b/inst/cov/pb/Tests/correlationRandomEffectsCovariates.txt new file mode 100644 index 0000000..958d661 --- /dev/null +++ b/inst/cov/pb/Tests/correlationRandomEffectsCovariates.txt @@ -0,0 +1,7 @@ +eta,covariate,statistics,p-value,test +eta_V,APGAR,1.65527,0.125934,Anova +eta_V,tAPGAR,0.0184744,0.981701,Anova +eta_V,WEIGHT,12.0595,<2.2e-16,Pearson +eta_k,APGAR,0.992395,0.458555,Anova +eta_k,tAPGAR,0.912807,0.407284,Anova +eta_k,WEIGHT,3.18816,0.00232602,Pearson diff --git a/inst/cov/pb/Tests/fixedEffects.txt b/inst/cov/pb/Tests/fixedEffects.txt new file mode 100644 index 0000000..81927d9 --- /dev/null +++ b/inst/cov/pb/Tests/fixedEffects.txt @@ -0,0 +1,3 @@ +parameter,statistics(sa),p-value(sa) +beta_V_tAPGAR_High,2.26508,0.0235 +beta_V_tAPGAR_Low,0.744812,0.456 diff --git a/inst/cov/pb/Tests/normalityIndividualParameters.txt b/inst/cov/pb/Tests/normalityIndividualParameters.txt new file mode 100644 index 0000000..ffe564c --- /dev/null +++ b/inst/cov/pb/Tests/normalityIndividualParameters.txt @@ -0,0 +1,3 @@ +parameter,statistics,p-value,test +V,0.115658,0.0172607,Kolmogorov-Smirnov +k,0.980138,0.672503,Shapiro-Wilk diff --git a/inst/cov/pb/Tests/normalityRandomEffects.txt b/inst/cov/pb/Tests/normalityRandomEffects.txt new file mode 100644 index 0000000..1b20300 --- /dev/null +++ b/inst/cov/pb/Tests/normalityRandomEffects.txt @@ -0,0 +1,3 @@ +eta,statistics,p-value +eta_V,0.95443,0.018648 +eta_k,0.980138,0.672503 diff --git a/inst/cov/pb/Tests/normalityResiduals.txt b/inst/cov/pb/Tests/normalityResiduals.txt new file mode 100644 index 0000000..ae548f5 --- /dev/null +++ b/inst/cov/pb/Tests/normalityResiduals.txt @@ -0,0 +1,4 @@ +residuals,statistics,p-value,test +IWRES_CONC,0.985979,0.0178589,Shapiro-Wilk +PWRES_CONC,0.917991,1.07147e-07,Shapiro-Wilk +NPDE_CONC,0.9481,1.68054e-05,Shapiro-Wilk diff --git a/inst/cov/pb/Tests/symmetryResiduals.txt b/inst/cov/pb/Tests/symmetryResiduals.txt new file mode 100644 index 0000000..d512a1c --- /dev/null +++ b/inst/cov/pb/Tests/symmetryResiduals.txt @@ -0,0 +1,4 @@ +residuals,statistics,p-value,test +IWRES_CONC,-0.855394,0.392333,Symmetry +PWRES_CONC,-1.06601,0.28642,Symmetry +NPDE_CONC,-4.22966,2.34047e-05,Symmetry diff --git a/inst/cov/pb/populationParameters.txt b/inst/cov/pb/populationParameters.txt new file mode 100644 index 0000000..bf4d263 --- /dev/null +++ b/inst/cov/pb/populationParameters.txt @@ -0,0 +1,8 @@ +parameter,value,CV,se_sa,rse_sa +V_pop,1.24689732935331,,0.0936975242081976,7.51445383693242 +beta_V_tAPGAR_High,0.260578209875729,,0.115041637466471,44.1486022646848 +beta_V_tAPGAR_Low,0.127948846160619,,0.17178681111809,134.262102608131 +k_pop,0.00479852739901777,,0.000243812155121,5.08097870131797 +omega_V,0.401481325663058,41.8216397185517,0.0390637761053152,9.72991110876708 +omega_k,0.186667045786903,18.8304995915346,0.069019120270078,36.9744536209511 +b,0.108861379047358,,0.00845666526279147,7.76828783246683 \ No newline at end of file diff --git a/inst/cov/pb/predictions.txt b/inst/cov/pb/predictions.txt new file mode 100644 index 0000000..45089cb --- /dev/null +++ b/inst/cov/pb/predictions.txt @@ -0,0 +1,156 @@ +id,time,CONC,popPred_medianCOV,popPred,indivPred_SAEM,indivPred_mean,indivPred_mode,indWRes_SAEM,indWRes_mean,indWRes_mode +1,2,17.3,19.8583,19.8583,18.1499,18.4203,18.1411,-0.430129,-0.558667,-0.425887 +1,112.5,31,31.5973,31.5973,29.4802,29.5874,29.3038,0.473565,0.438566,0.53171 +2,2,9.7,11.915,9.18174,12.0044,12.0672,11.7268,-1.76339,-1.802,-1.58769 +2,63.5,24.6,21.7614,16.7695,22.3403,22.2316,21.925,0.929176,0.978594,1.12074 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+57,109,27.8,46.0668,46.0668,28.3942,28.3999,28.4747,-0.192227,-0.194046,-0.217646 +58,8.5,22.4,21.5841,16.6329,22.103,22.34,21.9823,0.123437,0.0246723,0.174561 +58,47.5,27.9,25.4326,19.5985,25.8791,26.1415,25.7611,0.717346,0.617942,0.762691 +58,131.8,31,32.6869,25.1887,32.9564,33.2629,32.8493,-0.545318,-0.624917,-0.517127 +59,1.8,22.6,18.1281,18.1281,23.51,23.3269,23.1543,-0.355552,-0.286246,-0.219921 +59,73.8,34.3,25.31,25.31,33.0234,32.8308,32.6505,0.355095,0.41109,0.464079 +59,146.8,40.2,30.2466,30.2466,39.6285,39.4505,39.2857,0.132481,0.174515,0.213777 diff --git a/inst/cov/pb/summary.txt b/inst/cov/pb/summary.txt new file mode 100644 index 0000000..8feba16 --- /dev/null +++ b/inst/cov/pb/summary.txt @@ -0,0 +1,110 @@ +******************************************************************************** +* phenobarbital_project.mlxtran * +* May 09, 2024 at 20:48:29 * +* Monolix version : 2023R1 * +******************************************************************************** + + +ESTIMATION OF THE POPULATION PARAMETERS ________________________________________ + +Fixed Effects ---------------------------- se_sa rse(%) +V_pop : 1.25 0.0937 7.51 +beta_V_tAPGAR_High : 0.261 0.115 44.1 +beta_V_tAPGAR_Low : 0.128 0.172 134 +k_pop : 0.0048 0.000244 5.08 + +Standard Deviation of the Random Effects - +omega_V : 0.401 0.0391 9.73 +omega_k : 0.187 0.069 37 + +Error Model Parameters ------------------- +b : 0.109 0.00846 7.77 + +Elapsed time (seconds): 2.5 +CPU time (seconds): 2 +Exploratory phase iterations: 194 (Autostop) +Smoothing phase iterations: 89 (Autostop) + + _______________________________________________________________________________ + + + +ESTIMATION OF THE INDIVIDUAL PARAMETERS ________________________________________ + + +Estimation of the individual parameters by Conditional Distribution ------------ + min Q1 median Q3 max +V : 0.695 1.07 1.37 1.7 4.88 +k : 0.00344 0.00466 0.00485 0.00505 0.0063 + +Elapsed time (seconds): 0.67 +CPU time (seconds): 0.82 +Iterations: 78 (Autostop) + + ------------------------------------------------------------------------------- + + +Estimation of the individual parameters by Conditional Mode -------------------- + min Q1 median Q3 max +V : 0.692 1.06 1.37 1.68 4.94 +k : 0.00364 0.00464 0.0048 0.00498 0.00629 + +Elapsed time (seconds): 0.06 +CPU time (seconds): 0 + + ------------------------------------------------------------------------------- + + _______________________________________________________________________________ + + + +ESTIMATION OF THE FISHER INFORMATION MATRIX ____________________________________ + + +Estimation of the Fisher information matrix by Stochastic Approximation -------- + +Correlation Matrix : + V_pop 1 +beta_V_tAPGAR_High -0.64791 1 + beta_V_tAPGAR_Low -0.43591 0.28245 1 + k_pop -0.099287 0.0079791 0.032804 1 + omega_V -0.012152 0.013185 0.016219 0.022327 1 + omega_k 0.031777 0.020461 -0.03771 -0.43918 -0.075066 1 + b 0.0023841 -0.013771 0.018361 0.08753 -0.014211 -0.16785 1 + + min max max/min +Eigen values : 0.32 1.9 6 + +Elapsed time (seconds): 0.37 +CPU time (seconds): 0.4 +Iterations: 50 (Autostop) + + ------------------------------------------------------------------------------- + + _______________________________________________________________________________ + + + +ESTIMATION OF THE LOG-LIKELIHOOD _______________________________________________ + + (is) +-2 x log-likelihood (OFV) : 971.43 +Akaike Information Criteria (AIC) : 985.43 +Corrected Bayesian Information Criteria (BICc) : 1002.87 +Bayesian Information Criteria (BIC) : 999.97 + +Elapsed time (seconds) : 7.56 +CPU time (seconds) : 10.00 +MonteCarlo size (is): 10000 (Fixed number of iterations) + + +[Importance Sampling] Standard error : 0.070 + Sampling distribution : T-distribution with 5 degrees of freedom + + _______________________________________________________________________________ + +DATASET INFORMATION +Number of individuals: 59 +Number of observations (CONC): 155 +Number of doses: 589 + diff --git a/inst/cov/phenobarbital_project.mlxtran b/inst/cov/phenobarbital_project.mlxtran new file mode 100644 index 0000000..a12f485 --- /dev/null +++ b/inst/cov/phenobarbital_project.mlxtran @@ -0,0 +1,75 @@ + + +[FILEINFO] +file='data/phenobarbital_data.csv' +delimiter = semicolon +header = {ID, TIME, DOSE, WEIGHT, APGAR, CONC} + +[CONTENT] +ID = {use=identifier} +TIME = {use=time} +DOSE = {use=amount} +WEIGHT = {use=covariate, type=continuous} +APGAR = {use=covariate, type=categorical} +CONC = {use=observation, name=CONC, type=continuous} + + + +[COVARIATE] +input = APGAR + +APGAR = {type=categorical, categories={1, 10, 2, 3, 4, 5, 6, 7, 8, 9}} + +DEFINITION: +tAPGAR = +{ + transform = APGAR, + categories = { + High = {10, 8, 9}, + Low = {1, 2, 3}, + Med = {4, 5, 6, 7} }, + reference = Med +} + +[INDIVIDUAL] +input = {V_pop, omega_V, k_pop, omega_k, tAPGAR, beta_V_tAPGAR_High, beta_V_tAPGAR_Low} + +tAPGAR = {type=categorical, categories={High, Low, Med}} + +DEFINITION: +V = {distribution=logNormal, typical=V_pop, covariate=tAPGAR, coefficient={beta_V_tAPGAR_High, beta_V_tAPGAR_Low, 0}, sd=omega_V} +k = {distribution=logNormal, typical=k_pop, sd=omega_k} + +[LONGITUDINAL] +input = {b} + +file = 'lib:bolus_1cpt_Vk.txt' + +DEFINITION: +CONC = {distribution=normal, prediction=Cc, errorModel=proportional(b)} + + +data = CONC +model = CONC + + +V_pop = {value=1, method=MLE} +b = {value=0.3, method=MLE} +beta_V_tAPGAR_High = {value=0, method=MLE} +beta_V_tAPGAR_Low = {value=0, method=MLE} +k_pop = {value=0.01, method=MLE} +omega_V = {value=1, method=MLE} +omega_k = {value=1, method=MLE} + + + +[TASKS] +populationParameters() +individualParameters(method = {conditionalMean, conditionalMode }) +fim(method = StochasticApproximation) +logLikelihood(run = false,method = ImportanceSampling) +plotResult(method = {indfits, parameterdistribution, covariancemodeldiagnosis, covariatemodeldiagnosis, obspred, vpc, residualsscatter, residualsdistribution, randomeffects, saemresults }) + +[SETTINGS] +GLOBAL: +exportpath = 'pb' diff --git a/inst/cov/w1/FisherInformation/correlationEstimatesSA.txt b/inst/cov/w1/FisherInformation/correlationEstimatesSA.txt new file mode 100644 index 0000000..7ce7086 --- /dev/null +++ b/inst/cov/w1/FisherInformation/correlationEstimatesSA.txt @@ -0,0 +1,10 @@ +Tlag_pop,1,0.469324,0.0421566,-0.0484674,-0.899455,-0.503396,-0.035675,0.0622168,0.0881963,0.0661154 +ka_pop,0.469324,1,-0.0271025,-0.0833874,-0.448425,-0.110068,-0.041523,0.0368971,0.0368257,0.0576569 +V_pop,0.0421566,-0.0271025,1,0.00222496,-0.0200579,-0.026566,0.0376404,0.00307112,-0.0259787,0.0275584 +Cl_pop,-0.0484674,-0.0833874,0.00222496,1,0.0575445,0.0705647,-0.000467052,-0.00929513,0.0221508,-0.0328802 +omega_Tlag,-0.899455,-0.448425,-0.0200579,0.0575445,1,0.487733,0.0460069,-0.060085,-0.0929014,-0.065018 +omega_ka,-0.503396,-0.110068,-0.026566,0.0705647,0.487733,1,0.0263861,-0.0738753,-0.0702378,-0.0807465 +omega_V,-0.035675,-0.041523,0.0376404,-0.000467052,0.0460069,0.0263861,1,-0.00254901,-0.0231658,-0.00658089 +omega_Cl,0.0622168,0.0368971,0.00307112,-0.00929513,-0.060085,-0.0738753,-0.00254901,1,0.0416041,-0.033796 +a,0.0881963,0.0368257,-0.0259787,0.0221508,-0.0929014,-0.0702378,-0.0231658,0.0416041,1,-0.745283 +b,0.0661154,0.0576569,0.0275584,-0.0328802,-0.065018,-0.0807465,-0.00658089,-0.033796,-0.745283,1 diff --git a/inst/cov/w1/FisherInformation/covarianceEstimatesSA.txt b/inst/cov/w1/FisherInformation/covarianceEstimatesSA.txt new file mode 100644 index 0000000..902e9f1 --- /dev/null +++ b/inst/cov/w1/FisherInformation/covarianceEstimatesSA.txt @@ -0,0 +1,10 @@ +Tlag_pop,0.302671,0.101209,0.000960627,-0.00138107,-0.212874,-0.105277,-0.000601203,0.00126216,0.00192737,0.000282151 +ka_pop,0.101209,0.153645,-0.00044002,-0.00169293,-0.0756147,-0.0164006,-0.000498562,0.0005333,0.000573375,0.000175309 +V_pop,0.000960627,-0.00044002,0.00171557,4.77317e-06,-0.000357393,-0.000418281,4.77562e-05,4.69051e-06,-4.27414e-05,8.85426e-06 +Cl_pop,-0.00138107,-0.00169293,4.77317e-06,0.00268263,0.00128216,0.00138933,-7.40999e-07,-1.77524e-05,4.5572e-05,-1.32102e-05 +omega_Tlag,-0.212874,-0.0756147,-0.000357393,0.00128216,0.185061,0.0797587,0.000606251,-0.000953111,-0.00158748,-0.000216962 +omega_ka,-0.105277,-0.0164006,-0.000418281,0.00138933,0.0797587,0.144503,0.000307246,-0.00103552,-0.00106057,-0.000238098 +omega_V,-0.000601203,-0.000498562,4.77562e-05,-7.40999e-07,0.000606251,0.000307246,0.000938304,-2.87914e-06,-2.8187e-05,-1.56369e-06 +omega_Cl,0.00126216,0.0005333,4.69051e-06,-1.77524e-05,-0.000953111,-0.00103552,-2.87914e-06,0.00135969,6.09375e-05,-9.66671e-06 +a,0.00192737,0.000573375,-4.27414e-05,4.5572e-05,-0.00158748,-0.00106057,-2.8187e-05,6.09375e-05,0.00157782,-0.000229638 +b,0.000282151,0.000175309,8.85426e-06,-1.32102e-05,-0.000216962,-0.000238098,-1.56369e-06,-9.66671e-06,-0.000229638,6.0171e-05 diff --git a/inst/cov/w1/IndividualParameters/estimatedIndividualParameters.txt b/inst/cov/w1/IndividualParameters/estimatedIndividualParameters.txt new file mode 100644 index 0000000..ffd3201 --- /dev/null +++ b/inst/cov/w1/IndividualParameters/estimatedIndividualParameters.txt @@ -0,0 +1,33 @@ +id,Tlag_SAEM,ka_SAEM,V_SAEM,Cl_SAEM,Tlag_mean,ka_mean,V_mean,Cl_mean,Tlag_mode,ka_mode,V_mode,Cl_mode,Tlag_sd,ka_sd,V_sd,Cl_sd,wt,sex +1,0.89699,3.18356,7.7155,0.112121,0.831868,2.41434,7.70341,0.112094,0.773357,1.40624,7.66977,0.111513,0.52759,3.08441,0.602986,0.00632447,66.7,1 +2,0.718624,1.09983,8.49245,0.126091,0.773265,1.00002,8.39486,0.128054,0.608268,0.81841,8.31658,0.128488,0.185372,0.244834,0.419389,0.00555544,66.7,1 +3,0.984988,2.03157,8.50447,0.112731,0.761624,1.59214,8.54439,0.111233,0.809916,0.910516,8.45366,0.11257,0.377348,1.86541,0.359115,0.00487807,80,1 +4,0.789551,3.34704,5.09239,0.0717225,0.771295,3.38799,5.10436,0.0720395,0.807632,1.42138,5.08214,0.0724521,0.407529,3.34102,0.193445,0.00394699,40,0 +5,0.849642,2.84494,11.5478,0.17568,0.896895,2.67963,11.531,0.17574,0.731764,1.60891,11.533,0.175433,0.634691,3.82244,0.614687,0.00938912,75.3,1 +6,0.789369,4.95747,6.08682,0.230467,0.784412,3.15321,6.14972,0.231735,0.750412,1.56017,6.14308,0.231256,0.408823,2.76461,0.262255,0.0115726,60,0 +7,0.669423,5.98744,8.01958,0.1729,0.662361,6.42669,8.0165,0.172829,0.656685,3.65313,8.04694,0.173331,0.294273,5.06416,0.267207,0.00769139,90,1 +8,0.784203,0.387644,5.44763,0.110445,0.774173,0.364448,5.35042,0.110015,0.814392,0.37778,5.39832,0.110298,0.0662312,0.0511951,0.292947,0.00495156,50,0 +9,0.894139,2.37582,9.1685,0.116174,0.905689,2.96737,9.24133,0.115096,0.761808,1.4701,9.05823,0.115424,0.687818,4.44893,0.686241,0.00648725,70,1 +10,0.542691,0.292946,7.76953,0.283227,0.556388,0.29148,7.63686,0.287852,0.542705,0.285168,7.64338,0.28781,0.0785802,0.0425225,0.548988,0.0151928,66.7,1 +11,0.725429,1.93177,7.42821,0.130959,0.657124,1.66154,7.49539,0.132084,0.732436,1.54459,7.47479,0.130959,0.246634,0.68085,0.27629,0.00519396,82,1 +12,2.69552,0.678576,6.98318,0.134732,2.67233,0.673418,7.02019,0.134619,2.73951,0.742729,7.08755,0.134276,0.0977399,0.256928,0.329077,0.00488903,75.3,1 +13,1.38581,3.28407,8.91167,0.174143,1.41545,5.39446,8.87483,0.174636,1.37454,2.66191,8.92175,0.175493,0.0493199,3.03096,0.341627,0.00688878,75.3,1 +14,0.908167,3.32645,6.15584,0.156251,0.881501,2.76814,6.17709,0.155329,0.910186,2.79762,6.19507,0.155544,0.0514872,1.3331,0.247068,0.00807439,50,0 +15,0.490368,1.60658,6.74353,0.0984567,0.571118,2.34251,6.68033,0.0984256,0.605588,1.86275,6.74678,0.0978812,0.202167,1.5899,0.270946,0.00473518,56.7,0 +16,1.03506,2.86031,6.1256,0.0963757,0.947918,2.21712,6.04457,0.0971727,0.799485,1.26017,6.01044,0.0955013,0.637549,3.87122,0.395147,0.00480569,58,1 +17,0.938068,3.33694,10.98,0.150213,0.882651,3.54153,10.9094,0.15089,0.74268,1.57618,10.7469,0.149922,0.606295,5.31235,0.927394,0.00782076,78,1 +18,0.880379,4.04618,8.31304,0.178915,0.829533,3.02623,8.30686,0.180838,0.745832,1.55914,8.15841,0.178086,0.594091,6.87215,0.783178,0.0111682,74.7,1 +19,0.89667,2.68572,9.34696,0.186912,0.925721,2.82649,9.24069,0.185935,0.736833,1.60942,9.06206,0.184568,0.620313,3.82052,0.967679,0.0113016,63.7,1 +20,0.999854,2.64371,7.02631,0.0947927,0.948032,2.54399,7.06788,0.0949473,0.785931,1.33653,6.8836,0.0945344,0.584857,4.2717,0.516938,0.00539537,59,1 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b/inst/cov/w1/IndividualParameters/estimatedRandomEffects.txt new file mode 100644 index 0000000..b8fd942 --- /dev/null +++ b/inst/cov/w1/IndividualParameters/estimatedRandomEffects.txt @@ -0,0 +1,33 @@ +id,eta_Tlag_SAEM,eta_ka_SAEM,eta_V_SAEM,eta_Cl_SAEM,eta_Tlag_mean,eta_ka_mean,eta_V_mean,eta_Cl_mean,eta_Tlag_mode,eta_ka_mode,eta_V_mode,eta_Cl_mode,eta_Tlag_sd,eta_ka_sd,eta_V_sd,eta_Cl_sd,wt,sex +1,-0.0423976,0.138832,-0.0334843,-0.167792,-0.0841675,-0.0519486,-0.0358612,-0.168675,0.0117504,-0.0349136,-0.0371672,-0.172306,0.576789,1.06665,0.0784459,0.0557831,66.7,1 +2,-0.12308,-0.441893,0.0641598,-0.0500691,-0.0170326,-0.401013,0.0518995,-0.034933,-0.228374,-0.576227,0.0437969,-0.0306042,0.24037,0.218483,0.0505266,0.0434066,66.7,1 +3,0.089448,-0.0363632,0.0659581,-0.162062,-0.135233,-0.166529,0.0699274,-0.175786,0.0579405,-0.469579,0.0601456,-0.16287,0.535865,0.603511,0.0424146,0.044036,80,1 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+10,32,-0.941432,-0.788684,-0.0504749,-0.30918,62,1 diff --git a/inst/cov/w1/LogLikelihood/individualLL.txt b/inst/cov/w1/LogLikelihood/individualLL.txt new file mode 100644 index 0000000..37fb48b --- /dev/null +++ b/inst/cov/w1/LogLikelihood/individualLL.txt @@ -0,0 +1,33 @@ +id,importanceSampling +1,11.007136 +2,27.436454 +3,25.387680 +4,30.947486 +5,14.486862 +6,37.241838 +7,45.636552 +8,33.787292 +9,11.512947 +10,38.486309 +11,41.211130 +12,37.113185 +13,39.462364 +14,26.140391 +15,29.644207 +16,13.682642 +17,11.085054 +18,14.372758 +19,9.236523 +20,13.554236 +21,9.974623 +22,19.309946 +23,9.724362 +24,12.554324 +25,13.095378 +26,10.378976 +27,11.971067 +28,11.941267 +29,15.515808 +30,10.486635 +31,10.410935 +32,10.561945 diff --git a/inst/cov/w1/LogLikelihood/logLikelihood.txt b/inst/cov/w1/LogLikelihood/logLikelihood.txt new file mode 100644 index 0000000..5480e1a --- /dev/null +++ b/inst/cov/w1/LogLikelihood/logLikelihood.txt @@ -0,0 +1,6 @@ +criteria,importanceSampling +OFV,657.358312 +AIC,677.358312 +BIC,692.015671 +BICc,704.277586 +standardError,0.131188 diff --git a/inst/cov/w1/Tests/correlationRandomEffects.txt b/inst/cov/w1/Tests/correlationRandomEffects.txt new file mode 100644 index 0000000..3bad5d3 --- /dev/null +++ b/inst/cov/w1/Tests/correlationRandomEffects.txt @@ -0,0 +1,7 @@ +eta1,eta2,coeff,statistics,p-value +eta_Tlag,eta_ka,0,0.637709,0.528346 +eta_Tlag,eta_V,0,0.524268,0.603821 +eta_Tlag,eta_Cl,0,1.0463,0.303512 +eta_ka,eta_V,0,0.361813,0.719946 +eta_ka,eta_Cl,0,-0.581732,0.564954 +eta_V,eta_Cl,0,1.83107,0.0767172 diff --git a/inst/cov/w1/Tests/correlationRandomEffectsCovariates.txt b/inst/cov/w1/Tests/correlationRandomEffectsCovariates.txt new file mode 100644 index 0000000..05b0ffb --- /dev/null +++ b/inst/cov/w1/Tests/correlationRandomEffectsCovariates.txt @@ -0,0 +1,9 @@ +eta,covariate,statistics,p-value,test +eta_Tlag,sex,0.946024,0.338511,Anova +eta_Tlag,wt,1.12216,0.270697,Pearson +eta_ka,sex,0.151167,0.700168,Anova +eta_ka,wt,0.994976,0.327706,Pearson +eta_V,sex,18.1732,0.000184502,Anova +eta_V,wt,6.37812,4.87001e-07,Pearson +eta_Cl,sex,0.390628,0.536695,Anova +eta_Cl,wt,2.13068,0.041428,Pearson diff --git a/inst/cov/w1/Tests/normalityIndividualParameters.txt b/inst/cov/w1/Tests/normalityIndividualParameters.txt new file mode 100644 index 0000000..37a9c78 --- /dev/null +++ b/inst/cov/w1/Tests/normalityIndividualParameters.txt @@ -0,0 +1,5 @@ +parameter,statistics,p-value,test +Tlag,0.968623,0.529672,Shapiro-Wilk +ka,0.969788,0.797625,Shapiro-Wilk +V,0.978879,0.997045,Shapiro-Wilk +Cl,0.970709,0.765264,Shapiro-Wilk diff --git a/inst/cov/w1/Tests/normalityRandomEffects.txt b/inst/cov/w1/Tests/normalityRandomEffects.txt new file mode 100644 index 0000000..fb33f60 --- /dev/null +++ b/inst/cov/w1/Tests/normalityRandomEffects.txt @@ -0,0 +1,5 @@ +eta,statistics,p-value +eta_Tlag,0.968623,0.529672 +eta_ka,0.969788,0.797625 +eta_V,0.978879,0.997045 +eta_Cl,0.970709,0.765264 diff --git a/inst/cov/w1/Tests/normalityResiduals.txt b/inst/cov/w1/Tests/normalityResiduals.txt new file mode 100644 index 0000000..eb01539 --- /dev/null +++ b/inst/cov/w1/Tests/normalityResiduals.txt @@ -0,0 +1,4 @@ +residuals,statistics,p-value,test +IWRES_concentration,0.992359,0.103604,Shapiro-Wilk +PWRES_concentration,0.99082,0.122869,Shapiro-Wilk +NPDE_concentration,0.994731,0.551884,Shapiro-Wilk diff --git a/inst/cov/w1/Tests/symmetryResiduals.txt b/inst/cov/w1/Tests/symmetryResiduals.txt new file mode 100644 index 0000000..dcedf60 --- /dev/null +++ b/inst/cov/w1/Tests/symmetryResiduals.txt @@ -0,0 +1,4 @@ +residuals,statistics,p-value,test +IWRES_concentration,-0.206632,0.836297,Symmetry +PWRES_concentration,-0.510315,0.609831,Symmetry +NPDE_concentration,-2.2896,0.0220443,Symmetry diff --git a/inst/cov/w1/populationParameters.txt b/inst/cov/w1/populationParameters.txt new file mode 100644 index 0000000..9112f35 --- /dev/null +++ b/inst/cov/w1/populationParameters.txt @@ -0,0 +1,11 @@ +parameter,value,CV,se_sa,rse_sa +Tlag_pop,0.764322535850091,,0.420496337644856,55.0155618762665 +ka_pop,1.45620698534217,,0.570797523525994,39.1975542811912 +V_pop,7.96019644663432,,0.329706577234286,4.14194020769036 +Cl_pop,0.132481552644036,,0.00686176474906852,5.17941148191807 +omega_Tlag,0.605115662973185,66.4976041111586,0.430186959202578,71.091691312185 +omega_ka,1.08210228973354,149.165681014931,0.380135650264131,35.1293638199154 +omega_V,0.222522809015499,22.530606992046,0.0306317450105289,13.7656652574413 +omega_Cl,0.286211422517007,29.2174087265823,0.0368739656541468,12.8834710123967 +a,0.247145876284213,,0.0397217695323461,16.072195955504 +b,0.0503195895352995,,0.00775699508916458,15.4154577984445 \ No newline at end of file diff --git a/inst/cov/w1/predictions.txt b/inst/cov/w1/predictions.txt new file mode 100644 index 0000000..326fa85 --- /dev/null +++ b/inst/cov/w1/predictions.txt @@ -0,0 +1,248 @@ 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+32,120,2.5,1.6245,1.6245,2.44865,2.45311,2.43983,0.138639,0.126526,0.162661 diff --git a/inst/cov/w1/summary.txt b/inst/cov/w1/summary.txt new file mode 100644 index 0000000..318909f --- /dev/null +++ b/inst/cov/w1/summary.txt @@ -0,0 +1,121 @@ +******************************************************************************** +* warfarin_covariate1_project.mlxtran * +* May 09, 2024 at 20:53:44 * +* Monolix version : 2023R1 * +******************************************************************************** + + +ESTIMATION OF THE POPULATION PARAMETERS ________________________________________ + +Fixed Effects ---------------------------- se_sa rse(%) +Tlag_pop : 0.764 0.42 55 +ka_pop : 1.46 0.571 39.2 +V_pop : 7.96 0.33 4.14 +Cl_pop : 0.132 0.00686 5.18 + +Standard Deviation of the Random Effects - +omega_Tlag : 0.605 0.43 71.1 +omega_ka : 1.08 0.38 35.1 +omega_V : 0.223 0.0306 13.8 +omega_Cl : 0.286 0.0369 12.9 + +Error Model Parameters ------------------- +a : 0.247 0.0397 16.1 +b : 0.0503 0.00776 15.4 + +Elapsed time (seconds): 3.9 +CPU time (seconds): 5 +Exploratory phase iterations: 210 (Autostop) +Smoothing phase iterations: 95 (Autostop) + + _______________________________________________________________________________ + + + +ESTIMATION OF THE INDIVIDUAL PARAMETERS ________________________________________ + + +Estimation of the individual parameters by Conditional Distribution ------------ + min Q1 median Q3 max +Tlag : 0.556 0.779 0.89 0.949 2.67 +ka : 0.291 2.28 2.58 2.97 6.43 +V : 5.1 7.04 7.98 9.06 13 +Cl : 0.072 0.108 0.126 0.164 0.288 + +Elapsed time (seconds): 1.1 +CPU time (seconds): 1.4 +Iterations: 121 (Autostop) + + ------------------------------------------------------------------------------- + + +Estimation of the individual parameters by Conditional Mode -------------------- + min Q1 median Q3 max +Tlag : 0.543 0.74 0.763 0.791 2.74 +ka : 0.285 1.35 1.46 1.57 3.65 +V : 5.08 6.94 7.88 8.99 12.8 +Cl : 0.0725 0.108 0.127 0.164 0.288 + +Elapsed time (seconds): 0.076 +CPU time (seconds): 0 + + ------------------------------------------------------------------------------- + + _______________________________________________________________________________ + + + +ESTIMATION OF THE FISHER INFORMATION MATRIX ____________________________________ + + +Estimation of the Fisher information matrix by Stochastic Approximation -------- + +Correlation Matrix : + Tlag_pop 1 + ka_pop 0.46932 1 + V_pop 0.042157 -0.027102 1 + Cl_pop -0.048467 -0.083387 0.002225 1 +omega_Tlag -0.89945 -0.44843 -0.020058 0.057544 1 + omega_ka -0.5034 -0.11007 -0.026566 0.070565 0.48773 1 + omega_V -0.035675 -0.041523 0.03764-0.00046705 0.046007 0.026386 1 + omega_Cl 0.062217 0.036897 0.0030711-0.0092951 -0.060085 -0.073875 -0.002549 1 + a 0.088196 0.036826 -0.025979 0.022151 -0.092901 -0.070238 -0.023166 0.041604 1 + b 0.066115 0.057657 0.027558 -0.03288 -0.065018 -0.080747-0.0065809 -0.033796 -0.74528 1 + + min max max/min +Eigen values : 0.099 2.6 26 + +Elapsed time (seconds): 0.52 +CPU time (seconds): 0.67 +Iterations: 50 (Autostop) + + ------------------------------------------------------------------------------- + + _______________________________________________________________________________ + + + +ESTIMATION OF THE LOG-LIKELIHOOD _______________________________________________ + + (is) +-2 x log-likelihood (OFV) : 657.36 +Akaike Information Criteria (AIC) : 677.36 +Corrected Bayesian Information Criteria (BICc) : 704.28 +Bayesian Information Criteria (BIC) : 692.02 + +Elapsed time (seconds) : 4.03 +CPU time (seconds) : 5.00 +MonteCarlo size (is): 10000 (Fixed number of iterations) + + +[Importance Sampling] Standard error : 0.131 + Sampling distribution : T-distribution with 5 degrees of freedom + + _______________________________________________________________________________ + +DATASET INFORMATION +Number of individuals: 32 +Number of observations (obsid 1): 247 +Number of observations (obsid 2): 232 +Number of doses: 32 + diff --git a/inst/cov/w2/FisherInformation/correlationEstimatesLin.txt b/inst/cov/w2/FisherInformation/correlationEstimatesLin.txt new file mode 100644 index 0000000..82dd876 --- /dev/null +++ b/inst/cov/w2/FisherInformation/correlationEstimatesLin.txt @@ -0,0 +1,12 @@ +Tlag_pop,1,0.261827,0.0757948,0.000481349,0.0299138,0.00309266,0,0,0,0,0,0 +ka_pop,0.261827,1,-0.00812771,-0.0267474,-0.038648,-0.00495228,0,0,0,0,0,0 +V_pop,0.0757948,-0.00812771,1,0.108334,0.00287378,-0.000556425,0,0,0,0,0,0 +beta_V_lw70,0.000481349,-0.0267474,0.108334,1,0.00045024,-0.00281897,0,0,0,0,0,0 +Cl_pop,0.0299138,-0.038648,0.00287378,0.00045024,1,0.089524,0,0,0,0,0,0 +beta_Cl_lw70,0.00309266,-0.00495228,-0.000556425,-0.00281897,0.089524,1,0,0,0,0,0,0 +omega_Tlag,0,0,0,0,0,0,1,-0.0846999,-0.00177071,-0.000843516,-0.00239085,-0.00539952 +omega_ka,0,0,0,0,0,0,-0.0846999,1,-0.00249154,-0.00149518,0.0326994,-0.0590895 +omega_V,0,0,0,0,0,0,-0.00177071,-0.00249154,1,0.000697915,0.0062361,-0.0583388 +omega_Cl,0,0,0,0,0,0,-0.000843516,-0.00149518,0.000697915,1,-0.0100303,0.0013487 +a,0,0,0,0,0,0,-0.00239085,0.0326994,0.0062361,-0.0100303,1,-0.796461 +b,0,0,0,0,0,0,-0.00539952,-0.0590895,-0.0583388,0.0013487,-0.796461,1 diff --git a/inst/cov/w2/FisherInformation/covarianceEstimatesLin.txt b/inst/cov/w2/FisherInformation/covarianceEstimatesLin.txt new file mode 100644 index 0000000..dfcb716 --- /dev/null +++ b/inst/cov/w2/FisherInformation/covarianceEstimatesLin.txt @@ -0,0 +1,12 @@ +Tlag_pop,0.0522925,0.0180935,0.000473914,1.54432e-05,0.000326,0.000178914,0,0,0,0,0,0 +ka_pop,0.0180935,0.0913226,-6.7158e-05,-0.00113404,-0.0005566,-0.000378606,0,0,0,0,0,0 +V_pop,0.000473914,-6.7158e-05,0.000747619,0.000415589,3.74473e-06,-3.84893e-06,0,0,0,0,0,0 +beta_V_lw70,1.54432e-05,-0.00113404,0.000415589,0.0196842,3.01043e-06,-0.000100056,0,0,0,0,0,0 +Cl_pop,0.000326,-0.0005566,3.74473e-06,3.01043e-06,0.00227119,0.00107934,0,0,0,0,0,0 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b/inst/cov/w2/LogLikelihood/individualLL.txt @@ -0,0 +1,33 @@ +id,linearization +1,10.023007 +2,25.399805 +3,25.074543 +4,22.552924 +5,14.929574 +6,38.001445 +7,45.299347 +8,29.851534 +9,10.944949 +10,39.134500 +11,41.554462 +12,38.470126 +13,36.598471 +14,24.694871 +15,26.880481 +16,11.464666 +17,10.019696 +18,13.360782 +19,10.410076 +20,11.710218 +21,11.437087 +22,17.336472 +23,8.987713 +24,12.882689 +25,14.198689 +26,9.812692 +27,13.117082 +28,10.854955 +29,9.318614 +30,9.575680 +31,8.658680 +32,9.475203 diff --git a/inst/cov/w2/LogLikelihood/logLikelihood.txt b/inst/cov/w2/LogLikelihood/logLikelihood.txt new file mode 100644 index 0000000..de8b3cf --- /dev/null +++ b/inst/cov/w2/LogLikelihood/logLikelihood.txt @@ -0,0 +1,6 @@ +criteria,linearization +OFV,622.031033 +AIC,646.031033 +BIC,663.619863 +BICc,675.881778 +standardError, diff --git a/inst/cov/w2/Tests/correlationIndividualParametersCovariates.txt b/inst/cov/w2/Tests/correlationIndividualParametersCovariates.txt new file mode 100644 index 0000000..a5b34ff --- /dev/null +++ b/inst/cov/w2/Tests/correlationIndividualParametersCovariates.txt @@ -0,0 +1,3 @@ +parameter,covariate,statistics,p-value,test +V,beta_V_lw70,7.29371,4.02359e-08,t-Test +Cl,beta_Cl_lw70,2.38242,0.0237378,t-Test diff --git a/inst/cov/w2/Tests/correlationRandomEffects.txt b/inst/cov/w2/Tests/correlationRandomEffects.txt new file mode 100644 index 0000000..685fdaa --- /dev/null +++ b/inst/cov/w2/Tests/correlationRandomEffects.txt @@ -0,0 +1,7 @@ +eta1,eta2,coeff,statistics,p-value +eta_Tlag,eta_ka,0,-0.641528,0.525895 +eta_Tlag,eta_V,0,-0.573634,0.570354 +eta_Tlag,eta_Cl,0,-0.191715,0.849216 +eta_ka,eta_V,0,0.699169,0.489659 +eta_ka,eta_Cl,0,-0.158768,0.874881 +eta_V,eta_Cl,0,0.81866,0.419229 diff --git a/inst/cov/w2/Tests/correlationRandomEffectsCovariates.txt b/inst/cov/w2/Tests/correlationRandomEffectsCovariates.txt new file mode 100644 index 0000000..b090079 --- /dev/null +++ b/inst/cov/w2/Tests/correlationRandomEffectsCovariates.txt @@ -0,0 +1,13 @@ +eta,covariate,statistics,p-value,test +eta_Tlag,sex,0.453562,0.505804,Anova +eta_Tlag,lw70,-0.242794,0.809817,Pearson +eta_Tlag,wt,-0.391216,0.698402,Pearson +eta_ka,sex,0.0280049,0.86822,Anova +eta_ka,lw70,0.87679,0.387568,Pearson +eta_ka,wt,1.08569,0.286264,Pearson +eta_V,sex,0.401503,0.531116,Anova +eta_V,lw70,0.178538,0.859501,Pearson +eta_V,wt,0.196944,0.8452,Pearson +eta_Cl,sex,0.634432,0.431993,Anova +eta_Cl,lw70,0.0323859,0.974379,Pearson +eta_Cl,wt,-0.0465223,0.963202,Pearson diff --git a/inst/cov/w2/Tests/fixedEffects.txt b/inst/cov/w2/Tests/fixedEffects.txt new file mode 100644 index 0000000..e1c98e8 --- /dev/null +++ b/inst/cov/w2/Tests/fixedEffects.txt @@ -0,0 +1,3 @@ +parameter,statistics(lin),p-value(lin) +beta_V_lw70,6.40734,1.48e-10 +beta_Cl_lw70,2.35281,0.0186 diff --git a/inst/cov/w2/Tests/normalityIndividualParameters.txt b/inst/cov/w2/Tests/normalityIndividualParameters.txt new file mode 100644 index 0000000..554ce19 --- /dev/null +++ b/inst/cov/w2/Tests/normalityIndividualParameters.txt @@ -0,0 +1,5 @@ +parameter,statistics,p-value,test +Tlag,0.977027,0.959754,Shapiro-Wilk +ka,0.977932,0.998599,Shapiro-Wilk +V,0.0936126,0.0795308,Kolmogorov-Smirnov +Cl,0.0998117,0.319972,Kolmogorov-Smirnov diff --git a/inst/cov/w2/Tests/normalityRandomEffects.txt b/inst/cov/w2/Tests/normalityRandomEffects.txt new file mode 100644 index 0000000..54cbc63 --- /dev/null +++ b/inst/cov/w2/Tests/normalityRandomEffects.txt @@ -0,0 +1,5 @@ +eta,statistics,p-value +eta_Tlag,0.977027,0.959754 +eta_ka,0.977932,0.998599 +eta_V,0.965041,0.665704 +eta_Cl,0.89831,0.00611602 diff --git a/inst/cov/w2/Tests/normalityResiduals.txt b/inst/cov/w2/Tests/normalityResiduals.txt new file mode 100644 index 0000000..290abd8 --- /dev/null +++ b/inst/cov/w2/Tests/normalityResiduals.txt @@ -0,0 +1,4 @@ +residuals,statistics,p-value,test +IWRES_concentration,0.990539,0.0710422,Shapiro-Wilk +PWRES_concentration,0.979495,0.00122581,Shapiro-Wilk +NPDE_concentration,0.973912,0.000165811,Shapiro-Wilk diff --git a/inst/cov/w2/Tests/symmetryResiduals.txt b/inst/cov/w2/Tests/symmetryResiduals.txt new file mode 100644 index 0000000..65b3682 --- /dev/null +++ b/inst/cov/w2/Tests/symmetryResiduals.txt @@ -0,0 +1,4 @@ +residuals,statistics,p-value,test +IWRES_concentration,0.179912,0.857222,Symmetry +PWRES_concentration,-4.65912,3.17561e-06,Symmetry +NPDE_concentration,-4.46463,8.02065e-06,Symmetry diff --git a/inst/cov/w2/populationParameters.txt b/inst/cov/w2/populationParameters.txt new file mode 100644 index 0000000..d13bc63 --- /dev/null +++ b/inst/cov/w2/populationParameters.txt @@ -0,0 +1,13 @@ +parameter,value,CV,se_lin,rse_lin +Tlag_pop,0.780016055663023,,0.17837065691411,22.8675622276124 +ka_pop,1.35928759069304,,0.410771702678662,30.2196316284495 +V_pop,8.0607521386391,,0.22040205773655,2.73426169104066 +beta_V_lw70,0.898951301623242,,0.140300259496287,15.6071034374104 +Cl_pop,0.133622588749826,,0.00636805640551266,4.76570351247663 +beta_Cl_lw70,0.595223300469559,,0.252983840620238,42.5023416288751 +omega_Tlag,0.541595485175291,58.3848784310045,0.170849072479768,31.5455126854448 +omega_ka,0.850145400049819,102.960425004182,0.237536679119416,27.9407121541204 +omega_V,0.136594432002439,13.7234061647908,0.0214430916253883,15.6983643557341 +omega_Cl,0.263663140318272,26.8312553840452,0.0340742392287991,12.9233988443237 +a,0.238670616593435,,0.0426132443515246,17.8544158303803 +b,0.0526737305673756,,0.00870422703536792,16.5247969749062 \ No newline at end of file diff --git a/inst/cov/w2/predictions.txt b/inst/cov/w2/predictions.txt new file mode 100644 index 0000000..12e299a --- /dev/null +++ b/inst/cov/w2/predictions.txt @@ -0,0 +1,248 @@ +id,time,concentration,popPred_medianCOV,popPred,indivPred_SAEM,indivPred_mean,indivPred_mode,indWRes_SAEM,indWRes_mean,indWRes_mode +1,24,9.2,8.3931,8.87664,9.3554,9.31675,9.40839,-0.212447,-0.160063,-0.283814 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+******************************************************************************** +* warfarin_covariate2_project.mlxtran * +* May 09, 2024 at 20:54:57 * +* Monolix version : 2023R1 * +******************************************************************************** + + +ESTIMATION OF THE POPULATION PARAMETERS ________________________________________ + +Fixed Effects ---------------------------- se_lin rse(%) +Tlag_pop : 0.78 0.178 22.9 +ka_pop : 1.36 0.411 30.2 +V_pop : 8.06 0.22 2.73 +beta_V_lw70 : 0.899 0.14 15.6 +Cl_pop : 0.134 0.00637 4.77 +beta_Cl_lw70 : 0.595 0.253 42.5 + +Standard Deviation of the Random Effects - +omega_Tlag : 0.542 0.171 31.5 +omega_ka : 0.85 0.238 27.9 +omega_V : 0.137 0.0214 15.7 +omega_Cl : 0.264 0.0341 12.9 + +Error Model Parameters ------------------- +a : 0.239 0.0426 17.9 +b : 0.0527 0.0087 16.5 + +Elapsed time (seconds): 4.1 +CPU time (seconds): 5 +Exploratory phase iterations: 212 (Autostop) +Smoothing phase iterations: 97 (Autostop) + + _______________________________________________________________________________ + + + +ESTIMATION OF THE INDIVIDUAL PARAMETERS ________________________________________ + + +Estimation of the individual parameters by Conditional Distribution ------------ + min Q1 median Q3 max +Tlag : 0.555 0.821 0.882 0.933 2.77 +ka : 0.305 1.75 1.91 2.14 4.53 +V : 5.02 7.1 8.06 8.82 13.2 +Cl : 0.0717 0.108 0.127 0.163 0.282 + +Elapsed time (seconds): 0.74 +CPU time (seconds): 0.92 +Iterations: 77 (Autostop) + + ------------------------------------------------------------------------------- + + +Estimation of the individual parameters by Conditional Mode -------------------- + min Q1 median Q3 max +Tlag : 0.551 0.753 0.784 0.806 2.76 +ka : 0.291 1.25 1.34 1.5 3.34 +V : 5.01 7.02 7.97 8.75 13 +Cl : 0.0721 0.108 0.127 0.164 0.286 + +Elapsed time (seconds): 0.057 +CPU time (seconds): 0 + + ------------------------------------------------------------------------------- + + _______________________________________________________________________________ + + + +ESTIMATION OF THE FISHER INFORMATION MATRIX ____________________________________ + + +Estimation of the Fisher information matrix by Linearization ------------------- + +Correlation Matrix : + Tlag_pop 1 + ka_pop 0.26183 1 + V_pop 0.075795-0.0081277 1 + beta_V_lw700.00048135 -0.026747 0.10833 1 + Cl_pop 0.029914 -0.038648 0.00287380.00045024 1 +beta_Cl_lw70 0.0030927-0.0049523-0.00055643 -0.002819 0.089524 1 + omega_Tlag 0 0 0 0 0 0 1 + omega_ka 0 0 0 0 0 0 -0.0847 1 + omega_V 0 0 0 0 0 0-0.0017707-0.0024915 1 + omega_Cl 0 0 0 0 0 0-0.00084352-0.00149520.00069791 1 + a 0 0 0 0 0 0-0.0023909 0.032699 0.0062361 -0.01003 1 + b 0 0 0 0 0 0-0.0053995 -0.059089 -0.058339 0.0013487 -0.79646 1 + + min max max/min +Eigen values : 0.2 1.8 9 + +Elapsed time (seconds): 0.005 +CPU time (seconds): 0 + + ------------------------------------------------------------------------------- + + _______________________________________________________________________________ + + + +ESTIMATION OF THE LOG-LIKELIHOOD _______________________________________________ + + (lin) +-2 x log-likelihood (OFV) : 622.03 +Akaike Information Criteria (AIC) : 646.03 +Corrected Bayesian Information Criteria (BICc) : 675.88 +Bayesian Information Criteria (BIC) : 663.62 + +Elapsed time (seconds) : 0.00 +CPU time (seconds) : 0.00 + + _______________________________________________________________________________ + +DATASET INFORMATION +Number of individuals: 32 +Number of observations (obsid 1): 247 +Number of observations (obsid 2): 232 +Number of doses: 32 + diff --git a/inst/cov/w3/FisherInformation/correlationEstimatesSA.txt b/inst/cov/w3/FisherInformation/correlationEstimatesSA.txt new file mode 100644 index 0000000..0375137 --- /dev/null +++ b/inst/cov/w3/FisherInformation/correlationEstimatesSA.txt @@ -0,0 +1,12 @@ +Tlag_pop,1,0.0360747,-0.000248501,0.0299896,0.0167871,0.00133725,-0.74399,-0.191912,-0.0228334,-0.0216767,0.045628,-0.0222808 +ka_pop,0.0360747,1,-0.0699077,0.0388781,-0.059607,0.018762,0.0378008,0.148057,0.0265794,0.0126461,-0.0238185,0.0202836 +V_pop,-0.000248501,-0.0699077,1,-0.416163,0.00729685,-0.00300831,0.029266,0.0217827,0.00610173,-0.00388959,-0.0312685,0.0454156 +beta_V_tSex_F,0.0299896,0.0388781,-0.416163,1,-0.00394288,-0.000107724,-0.0410955,-0.0197238,-0.000791073,0.00325253,-0.00017444,-0.00756661 +Cl_pop,0.0167871,-0.059607,0.00729685,-0.00394288,1,-0.396499,0.000789918,0.0372423,-0.01383,-0.00155349,0.0171267,-0.013832 +beta_Cl_tSex_F,0.00133725,0.018762,-0.00300831,-0.000107724,-0.396499,1,-0.00715013,-0.0195038,0.00584487,-0.0060485,0.0096107,-0.00437649 +omega_Tlag,-0.74399,0.0378008,0.029266,-0.0410955,0.000789918,-0.00715013,1,0.155201,0.0338494,0.0152551,-0.0587083,0.0220399 +omega_ka,-0.191912,0.148057,0.0217827,-0.0197238,0.0372423,-0.0195038,0.155201,1,-0.0375831,-0.0203223,-0.039965,0.0205156 +omega_V,-0.0228334,0.0265794,0.00610173,-0.000791073,-0.01383,0.00584487,0.0338494,-0.0375831,1,0.00332933,-0.0364158,-0.022802 +omega_Cl,-0.0216767,0.0126461,-0.00388959,0.00325253,-0.00155349,-0.0060485,0.0152551,-0.0203223,0.00332933,1,0.0413831,-0.047834 +a,0.045628,-0.0238185,-0.0312685,-0.00017444,0.0171267,0.0096107,-0.0587083,-0.039965,-0.0364158,0.0413831,1,-0.746091 +b,-0.0222808,0.0202836,0.0454156,-0.00756661,-0.013832,-0.00437649,0.0220399,0.0205156,-0.022802,-0.047834,-0.746091,1 diff --git a/inst/cov/w3/FisherInformation/covarianceEstimatesSA.txt b/inst/cov/w3/FisherInformation/covarianceEstimatesSA.txt new file mode 100644 index 0000000..f9b33a0 --- /dev/null +++ b/inst/cov/w3/FisherInformation/covarianceEstimatesSA.txt @@ -0,0 +1,12 @@ +Tlag_pop,0.116829,0.00381408,-3.00146e-06,0.00087222,0.000321585,6.45183e-05,-0.0869622,-0.0172905,-0.000199902,-0.00027062,0.000596188,-5.73116e-05 +ka_pop,0.00381408,0.0956804,-0.000764125,0.00102328,-0.00103337,0.000819193,0.00399853,0.0120718,0.000210585,0.000142875,-0.000281646,4.72163e-05 +V_pop,-3.00146e-06,-0.000764125,0.00124869,-0.00125133,1.44514e-05,-1.50053e-05,0.000353655,0.000202894,5.5227e-06,-5.0202e-06,-4.22388e-05,1.20773e-05 +beta_V_tSex_F,0.00087222,0.00102328,-0.00125133,0.00724034,-1.88035e-05,-1.29385e-06,-0.00119581,-0.000442385,-1.72411e-06,1.01086e-05,-5.67417e-07,-4.84525e-06 +Cl_pop,0.000321585,-0.00103337,1.44514e-05,-1.88035e-05,0.00314118,-0.00313677,1.51396e-05,0.000550191,-1.98536e-05,-3.18012e-06,3.6694e-05,-5.83399e-06 +beta_Cl_tSex_F,6.45183e-05,0.000819193,-1.50053e-05,-1.29385e-06,-0.00313677,0.0199246,-0.00034514,-0.000725679,2.11319e-05,-3.1184e-05,5.18592e-05,-4.64896e-06 +omega_Tlag,-0.0869622,0.00399853,0.000353655,-0.00119581,1.51396e-05,-0.00034514,0.116943,0.0139898,0.000296489,0.000190543,-0.000767474,5.67197e-05 +omega_ka,-0.0172905,0.0120718,0.000202894,-0.000442385,0.000550191,-0.000725679,0.0139898,0.0694802,-0.000253742,-0.000195656,-0.000402704,4.06959e-05 +omega_V,-0.000199902,0.000210585,5.5227e-06,-1.72411e-06,-1.98536e-05,2.11319e-05,0.000296489,-0.000253742,0.000656055,3.1147e-06,-3.56563e-05,-4.39519e-06 +omega_Cl,-0.00027062,0.000142875,-5.0202e-06,1.01086e-05,-3.18012e-06,-3.1184e-05,0.000190543,-0.000195656,3.1147e-06,0.00133407,5.77815e-05,-1.31481e-05 +a,0.000596188,-0.000281646,-4.22388e-05,-5.67417e-07,3.6694e-05,5.18592e-05,-0.000767474,-0.000402704,-3.56563e-05,5.77815e-05,0.00146135,-0.000214637 +b,-5.73116e-05,4.72163e-05,1.20773e-05,-4.84525e-06,-5.83399e-06,-4.64896e-06,5.67197e-05,4.06959e-05,-4.39519e-06,-1.31481e-05,-0.000214637,5.66332e-05 diff --git a/inst/cov/w3/IndividualParameters/estimatedIndividualParameters.txt b/inst/cov/w3/IndividualParameters/estimatedIndividualParameters.txt new file mode 100644 index 0000000..5b39f29 --- /dev/null +++ b/inst/cov/w3/IndividualParameters/estimatedIndividualParameters.txt @@ -0,0 +1,33 @@ +id,Tlag_SAEM,ka_SAEM,V_SAEM,Cl_SAEM,Tlag_mean,ka_mean,V_mean,Cl_mean,Tlag_mode,ka_mode,V_mode,Cl_mode,Tlag_sd,ka_sd,V_sd,Cl_sd,wt,lw70,sex,tSex +1,0.971633,2.28578,7.82804,0.111806,0.839088,1.96192,7.77659,0.111857,0.789401,1.34988,7.78501,0.111583,0.588187,1.90053,0.572476,0.00608059,66.7,-0.048290289127781,1,M +2,0.671624,0.936021,8.47443,0.127869,0.781163,0.997549,8.44499,0.128245,0.619934,0.833541,8.35059,0.128493,0.223854,0.278555,0.357605,0.00598566,66.7,-0.048290289127781,1,M +3,0.85069,1.79501,8.50568,0.111792,0.834251,1.38663,8.52901,0.111943,0.828733,0.927394,8.47582,0.112589,0.397999,0.949563,0.320265,0.0047526,80,0.1335313926245226,1,M 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+10,32,0.760497,0.407706,-0.097495,-0.232856,62,-0.1213608570042675,1,M diff --git a/inst/cov/w3/LogLikelihood/individualLL.txt b/inst/cov/w3/LogLikelihood/individualLL.txt new file mode 100644 index 0000000..1435d8f --- /dev/null +++ b/inst/cov/w3/LogLikelihood/individualLL.txt @@ -0,0 +1,33 @@ +id,importanceSampling +1,10.837151 +2,26.687592 +3,24.705213 +4,25.831011 +5,14.522919 +6,36.320657 +7,45.049469 +8,30.124861 +9,10.913020 +10,38.209190 +11,40.845405 +12,36.929049 +13,38.296788 +14,24.869719 +15,28.862496 +16,15.604586 +17,10.840437 +18,13.776348 +19,8.527822 +20,14.130230 +21,9.305481 +22,20.843286 +23,9.381334 +24,12.581540 +25,13.551815 +26,9.865159 +27,11.983694 +28,11.312150 +29,16.490579 +30,10.212287 +31,9.814127 +32,10.457273 diff --git a/inst/cov/w3/LogLikelihood/logLikelihood.txt b/inst/cov/w3/LogLikelihood/logLikelihood.txt new file mode 100644 index 0000000..146e381 --- /dev/null +++ b/inst/cov/w3/LogLikelihood/logLikelihood.txt @@ -0,0 +1,6 @@ +criteria,importanceSampling +OFV,641.682690 +AIC,665.682690 +BIC,683.271520 +BICc,695.533435 +standardError,0.097109 diff --git a/inst/cov/w3/Tests/correlationIndividualParametersCovariates.txt b/inst/cov/w3/Tests/correlationIndividualParametersCovariates.txt new file mode 100644 index 0000000..69a7a83 --- /dev/null +++ b/inst/cov/w3/Tests/correlationIndividualParametersCovariates.txt @@ -0,0 +1,3 @@ +parameter,covariate,statistics,p-value,test +V,beta_V_tSex_F,-4.6112,6.96781e-05,t-Test +Cl,beta_Cl_tSex_F,-0.709272,0.483632,t-Test diff --git a/inst/cov/w3/Tests/correlationRandomEffects.txt b/inst/cov/w3/Tests/correlationRandomEffects.txt new file mode 100644 index 0000000..daa19aa --- /dev/null +++ b/inst/cov/w3/Tests/correlationRandomEffects.txt @@ -0,0 +1,7 @@ +eta1,eta2,coeff,statistics,p-value +eta_Tlag,eta_ka,0,0.0267898,0.978799 +eta_Tlag,eta_V,0,-1.18134,0.246453 +eta_Tlag,eta_Cl,0,0.385404,0.70257 +eta_ka,eta_V,0,1.95311,0.0598845 +eta_ka,eta_Cl,0,0.155127,0.877727 +eta_V,eta_Cl,0,2.27774,0.0297911 diff --git a/inst/cov/w3/Tests/correlationRandomEffectsCovariates.txt b/inst/cov/w3/Tests/correlationRandomEffectsCovariates.txt new file mode 100644 index 0000000..720696e --- /dev/null +++ b/inst/cov/w3/Tests/correlationRandomEffectsCovariates.txt @@ -0,0 +1,17 @@ +eta,covariate,statistics,p-value,test +eta_Tlag,sex,0.831564,0.369091,Anova +eta_Tlag,tSex,0.831564,0.369091,Anova +eta_Tlag,lw70,-0.00221955,0.998244,Pearson +eta_Tlag,wt,-0.113675,0.910253,Pearson +eta_ka,sex,0.00643776,0.936583,Anova +eta_ka,tSex,0.00643776,0.936583,Anova +eta_ka,lw70,0.839816,0.407655,Pearson +eta_ka,wt,1.00595,0.322484,Pearson +eta_V,sex,0.00303627,0.956422,Anova +eta_V,tSex,0.00303627,0.956422,Anova +eta_V,lw70,2.41485,0.0220458,Pearson +eta_V,wt,2.62629,0.0134608,Pearson +eta_Cl,sex,0.00275292,0.958503,Anova +eta_Cl,tSex,0.00275292,0.958503,Anova +eta_Cl,lw70,1.73205,0.0935372,Pearson +eta_Cl,wt,1.66017,0.107299,Pearson diff --git a/inst/cov/w3/Tests/fixedEffects.txt b/inst/cov/w3/Tests/fixedEffects.txt new file mode 100644 index 0000000..65feedf --- /dev/null +++ b/inst/cov/w3/Tests/fixedEffects.txt @@ -0,0 +1,3 @@ +parameter,statistics(sa),p-value(sa) +beta_V_tSex_F,4.49263,7.03e-06 +beta_Cl_tSex_F,0.664779,0.506 diff --git a/inst/cov/w3/Tests/normalityIndividualParameters.txt b/inst/cov/w3/Tests/normalityIndividualParameters.txt new file mode 100644 index 0000000..065cb79 --- /dev/null +++ b/inst/cov/w3/Tests/normalityIndividualParameters.txt @@ -0,0 +1,5 @@ +parameter,statistics,p-value,test +Tlag,0.972932,0.668331,Shapiro-Wilk +ka,0.974204,0.866384,Shapiro-Wilk +V,0.0954507,0.299865,Kolmogorov-Smirnov +Cl,0.10989,0.220282,Kolmogorov-Smirnov diff --git a/inst/cov/w3/Tests/normalityRandomEffects.txt b/inst/cov/w3/Tests/normalityRandomEffects.txt new file mode 100644 index 0000000..67a2df1 --- /dev/null +++ b/inst/cov/w3/Tests/normalityRandomEffects.txt @@ -0,0 +1,5 @@ +eta,statistics,p-value +eta_Tlag,0.972932,0.668331 +eta_ka,0.974204,0.866384 +eta_V,0.96511,0.619619 +eta_Cl,0.950778,0.257498 diff --git a/inst/cov/w3/Tests/normalityResiduals.txt b/inst/cov/w3/Tests/normalityResiduals.txt new file mode 100644 index 0000000..5955e4f --- /dev/null +++ b/inst/cov/w3/Tests/normalityResiduals.txt @@ -0,0 +1,4 @@ +residuals,statistics,p-value,test +IWRES_concentration,0.990847,0.0290732,Shapiro-Wilk +PWRES_concentration,0.994961,0.592559,Shapiro-Wilk +NPDE_concentration,0.992062,0.205396,Shapiro-Wilk diff --git a/inst/cov/w3/Tests/symmetryResiduals.txt b/inst/cov/w3/Tests/symmetryResiduals.txt new file mode 100644 index 0000000..6d9f397 --- /dev/null +++ b/inst/cov/w3/Tests/symmetryResiduals.txt @@ -0,0 +1,4 @@ +residuals,statistics,p-value,test +IWRES_concentration,0.0824229,0.93431,Symmetry +PWRES_concentration,-1.44732,0.147808,Symmetry +NPDE_concentration,-2.52424,0.0115948,Symmetry diff --git a/inst/cov/w3/populationParameters.txt b/inst/cov/w3/populationParameters.txt new file mode 100644 index 0000000..d2df296 --- /dev/null +++ b/inst/cov/w3/populationParameters.txt @@ -0,0 +1,13 @@ +parameter,value,CV,se_sa,rse_sa +Tlag_pop,0.771438750805779,,0.263679942425076,34.1802822517872 +ka_pop,1.42775873640368,,0.441637834721607,30.9322453059561 +V_pop,8.46609504205801,,0.299165215219173,3.5336859996607 +beta_V_tSex_F,-0.382278567256413,,0.0850901726087562,22.2586825150681 +Cl_pop,0.134437806143132,,0.00753472722343848,5.60461929542086 +beta_Cl_tSex_F,-0.0938365059053137,,0.141154435818998,150.425929074374 +omega_Tlag,0.61940678586983,68.385184978931,0.34196954759751,55.2092026433459 +omega_ka,0.992834041241909,129.604748563596,0.26359089754432,26.5493412388038 +omega_V,0.166818280322244,16.7985605874085,0.025613564608197,15.3541713526355 +omega_Cl,0.285345299602576,29.1253382073524,0.0365249350085803,12.8002581642143 +a,0.24818990819019,,0.0382275439573807,15.402537611677 +b,0.0508665778176092,,0.00752550584274643,14.7945982718366 \ No newline at end of file diff --git a/inst/cov/w3/predictions.txt b/inst/cov/w3/predictions.txt new file mode 100644 index 0000000..3f727e5 --- /dev/null +++ b/inst/cov/w3/predictions.txt @@ -0,0 +1,248 @@ +id,time,concentration,popPred_medianCOV,popPred,indivPred_SAEM,indivPred_mean,indivPred_mode,indWRes_SAEM,indWRes_mean,indWRes_mode +1,24,9.2,8.26001,8.26001,9.25179,9.28379,9.30886,-0.0720454,-0.116308,-0.150843 +1,36,8.5,6.8269,6.8269,7.79454,7.81203,7.8379,1.0943,1.06569,1.02354 +1,48,6.4,5.64244,5.64244,6.56682,6.57359,6.59937,-0.286527,-0.297974,-0.34146 +1,72,4.8,3.85437,3.85437,4.66106,4.65457,4.67852,0.286302,0.29988,0.249872 +1,96,3.1,2.63293,2.63293,3.30837,3.29577,3.31676,-0.500327,-0.470791,-0.519935 +1,120,2.5,1.79856,1.79856,2.34825,2.33364,2.35137,0.412772,0.453422,0.404121 +2,0.5,0.02,0,0,0,0,0,0.0805835,0.0805835,0.0805835 +2,2,8.4,9.6467,9.6467,8.29654,8.23915,8.08229,0.154377,0.241047,0.481876 +2,3,9.7,11.0335,11.0335,10.2229,10.3114,10.0837,-0.680717,-0.791223,-0.504158 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+32,96,3.5,2.44863,2.44863,3.40135,3.3664,3.39485,0.234216,0.31853,0.249841 +32,120,2.5,1.67267,1.67267,2.47979,2.4526,2.46373,0.0539968,0.127085,0.0971117 diff --git a/inst/cov/w3/summary.txt b/inst/cov/w3/summary.txt new file mode 100644 index 0000000..f35ffe7 --- /dev/null +++ b/inst/cov/w3/summary.txt @@ -0,0 +1,125 @@ +******************************************************************************** +* warfarin_covariate3_project.mlxtran * +* May 09, 2024 at 20:57:01 * +* Monolix version : 2023R1 * +******************************************************************************** + + +ESTIMATION OF THE POPULATION PARAMETERS ________________________________________ + +Fixed Effects ---------------------------- se_sa rse(%) +Tlag_pop : 0.771 0.264 34.2 +ka_pop : 1.43 0.442 30.9 +V_pop : 8.47 0.299 3.53 +beta_V_tSex_F : -0.382 0.0851 22.3 +Cl_pop : 0.134 0.00753 5.6 +beta_Cl_tSex_F : -0.0938 0.141 150 + +Standard Deviation of the Random Effects - +omega_Tlag : 0.619 0.342 55.2 +omega_ka : 0.993 0.264 26.5 +omega_V : 0.167 0.0256 15.4 +omega_Cl : 0.285 0.0365 12.8 + +Error Model Parameters ------------------- +a : 0.248 0.0382 15.4 +b : 0.0509 0.00753 14.8 + +Elapsed time (seconds): 3.9 +CPU time (seconds): 5 +Exploratory phase iterations: 194 (Autostop) +Smoothing phase iterations: 94 (Autostop) + + _______________________________________________________________________________ + + + +ESTIMATION OF THE INDIVIDUAL PARAMETERS ________________________________________ + + +Estimation of the individual parameters by Conditional Distribution ------------ + min Q1 median Q3 max +Tlag : 0.457 0.785 0.897 0.999 2.77 +ka : 0.313 1.82 2.28 2.57 5.48 +V : 5.07 7.16 8.05 9 12.5 +Cl : 0.072 0.108 0.127 0.164 0.287 + +Elapsed time (seconds): 0.7 +CPU time (seconds): 0.89 +Iterations: 78 (Autostop) + + ------------------------------------------------------------------------------- + + +Estimation of the individual parameters by Conditional Mode -------------------- + min Q1 median Q3 max +Tlag : 0.549 0.741 0.772 0.807 2.75 +ka : 0.293 1.28 1.42 1.55 3.51 +V : 5.05 7.09 7.97 9 12.4 +Cl : 0.0724 0.108 0.127 0.164 0.287 + +Elapsed time (seconds): 0.061 +CPU time (seconds): 0 + + ------------------------------------------------------------------------------- + + _______________________________________________________________________________ + + + +ESTIMATION OF THE FISHER INFORMATION MATRIX ____________________________________ + + +Estimation of the Fisher information matrix by Stochastic Approximation -------- + +Correlation Matrix : + Tlag_pop 1 + ka_pop 0.036075 1 + V_pop-0.0002485 -0.069908 1 + beta_V_tSex_F 0.02999 0.038878 -0.41616 1 + Cl_pop 0.016787 -0.059607 0.0072968-0.0039429 1 +beta_Cl_tSex_F 0.0013373 0.018762-0.0030083-0.00010772 -0.3965 1 + omega_Tlag -0.74399 0.037801 0.029266 -0.0410960.00078992-0.0071501 1 + omega_ka -0.19191 0.14806 0.021783 -0.019724 0.037242 -0.019504 0.1552 1 + omega_V -0.022833 0.026579 0.0061017-0.00079107 -0.01383 0.0058449 0.033849 -0.037583 1 + omega_Cl -0.021677 0.012646-0.0038896 0.0032525-0.0015535-0.0060485 0.015255 -0.020322 0.0033293 1 + a 0.045628 -0.023819 -0.031269-0.00017444 0.017127 0.0096107 -0.058708 -0.039965 -0.036416 0.041383 1 + b -0.022281 0.020284 0.045416-0.0075666 -0.013832-0.0043765 0.02204 0.020516 -0.022802 -0.047834 -0.74609 1 + + min max max/min +Eigen values : 0.24 1.9 7.8 + +Elapsed time (seconds): 0.66 +CPU time (seconds): 0.85 +Iterations: 50 (Autostop) + + ------------------------------------------------------------------------------- + + _______________________________________________________________________________ + + + +ESTIMATION OF THE LOG-LIKELIHOOD _______________________________________________ + + (is) +-2 x log-likelihood (OFV) : 641.68 +Akaike Information Criteria (AIC) : 665.68 +Corrected Bayesian Information Criteria (BICc) : 695.53 +Bayesian Information Criteria (BIC) : 683.27 + +Elapsed time (seconds) : 4.67 +CPU time (seconds) : 7.00 +MonteCarlo size (is): 10000 (Fixed number of iterations) + + +[Importance Sampling] Standard error : 0.097 + Sampling distribution : T-distribution with 5 degrees of freedom + + _______________________________________________________________________________ + +DATASET INFORMATION +Number of individuals: 32 +Number of observations (obsid 1): 247 +Number of observations (obsid 2): 232 +Number of doses: 32 + diff --git a/inst/cov/warfarin_covariate1_project.mlxtran b/inst/cov/warfarin_covariate1_project.mlxtran new file mode 100644 index 0000000..ff2410d --- /dev/null +++ b/inst/cov/warfarin_covariate1_project.mlxtran @@ -0,0 +1,72 @@ + + +[FILEINFO] +file='data/warfarin_data.csv' +delimiter = comma +header={id, time, amt, dv, dvid, wt, sex, age} + +[CONTENT] +id = {use=identifier} +time = {use=time} +amt = {use=amount} +dv = {use=observation, yname={'1', '2'}, type={continuous, continuous}} +dvid = {use=observationtype} +wt = {use=covariate, type=continuous} +sex = {use=covariate, type=categorical} + +[SETTINGS] +dataType = {'1'=plasma, '2'=plasma} + + + +[COVARIATE] +input = {wt, sex} + +sex = {type=categorical, categories={'0', '1'}} + +[INDIVIDUAL] +input = {Tlag_pop, omega_Tlag, ka_pop, omega_ka, V_pop, omega_V, Cl_pop, omega_Cl} + +DEFINITION: +Tlag = {distribution=logNormal, typical=Tlag_pop, sd=omega_Tlag} +ka = {distribution=logNormal, typical=ka_pop, sd=omega_ka} +V = {distribution=logNormal, typical=V_pop, sd=omega_V} +Cl = {distribution=logNormal, typical=Cl_pop, sd=omega_Cl} + +[LONGITUDINAL] +input = {a, b} + +file = 'lib:oral1_1cpt_TlagkaVCl.txt' + +DEFINITION: +concentration = {distribution=normal, prediction=Cc, errorModel=combined1(a, b)} + + +data = '1' +model = concentration + + +Cl_pop = {value=0.1, method=MLE} +Tlag_pop = {value=1, method=MLE} +V_pop = {value=5, method=MLE} +a = {value=1, method=MLE} +b = {value=0.3, method=MLE} +c = {value=1, method=FIXED} +ka_pop = {value=1, method=MLE} +omega_Cl = {value=1, method=MLE} +omega_Tlag = {value=1, method=MLE} +omega_V = {value=1, method=MLE} +omega_ka = {value=1, method=MLE} + + + +[TASKS] +populationParameters() +individualParameters(method = {conditionalMean, conditionalMode }) +fim(run = false,method = StochasticApproximation) +logLikelihood(run = false,method = ImportanceSampling) +plotResult(method = {indfits, parameterdistribution, covariancemodeldiagnosis, covariatemodeldiagnosis, obspred, vpc, residualsscatter, residualsdistribution, randomeffects, saemresults }) + +[SETTINGS] +GLOBAL: +exportpath = 'w1' diff --git a/inst/cov/warfarin_covariate2_project.mlxtran b/inst/cov/warfarin_covariate2_project.mlxtran new file mode 100644 index 0000000..44d86e8 --- /dev/null +++ b/inst/cov/warfarin_covariate2_project.mlxtran @@ -0,0 +1,77 @@ + + +[FILEINFO] +file='data/warfarin_data.csv' +delimiter = comma +header={id, time, amt, dv, dvid, wt, sex, age} + +[CONTENT] +id = {use=identifier} +time = {use=time} +amt = {use=amount} +dv = {use=observation, yname={'1', '2'}, type={continuous, continuous}} +dvid = {use=observationtype} +wt = {use=covariate, type=continuous} +sex = {use=covariate, type=categorical} + +[SETTINGS] +dataType = {'1'=plasma, '2'=plasma} + + + +[COVARIATE] +input = {wt, sex} + +sex = {type=categorical, categories={'0', '1'}} + +EQUATION: +lw70 = log(wt/70) + +[INDIVIDUAL] +input = {Tlag_pop, omega_Tlag, ka_pop, omega_ka, V_pop, omega_V, Cl_pop, omega_Cl, lw70, beta_V_lw70, beta_Cl_lw70} + +DEFINITION: +Tlag = {distribution=logNormal, typical=Tlag_pop, sd=omega_Tlag} +ka = {distribution=logNormal, typical=ka_pop, sd=omega_ka} +V = {distribution=logNormal, typical=V_pop, covariate=lw70, coefficient=beta_V_lw70, sd=omega_V} +Cl = {distribution=logNormal, typical=Cl_pop, covariate=lw70, coefficient=beta_Cl_lw70, sd=omega_Cl} + +[LONGITUDINAL] +input = {a, b} + +file = 'lib:oral1_1cpt_TlagkaVCl.txt' + +DEFINITION: +concentration = {distribution=normal, prediction=Cc, errorModel=combined1(a, b)} + + +data = '1' +model = concentration + + +Cl_pop = {value=0.1, method=MLE} +Tlag_pop = {value=1, method=MLE} +V_pop = {value=5, method=MLE} +a = {value=1, method=MLE} +b = {value=0.3, method=MLE} +beta_Cl_lw70 = {value=0, method=MLE} +beta_V_lw70 = {value=0, method=MLE} +c = {value=1, method=FIXED} +ka_pop = {value=1, method=MLE} +omega_Cl = {value=1, method=MLE} +omega_Tlag = {value=1, method=MLE} +omega_V = {value=1, method=MLE} +omega_ka = {value=1, method=MLE} + + + +[TASKS] +populationParameters() +individualParameters(method = {conditionalMean, conditionalMode }) +fim(method = Linearization) +logLikelihood(method = Linearization) +plotResult(method = {indfits, parameterdistribution, covariancemodeldiagnosis, covariatemodeldiagnosis, obspred, vpc, residualsscatter, residualsdistribution, randomeffects, saemresults }) + +[SETTINGS] +GLOBAL: +exportpath = 'w2' diff --git a/inst/cov/warfarin_covariate3_project.mlxtran b/inst/cov/warfarin_covariate3_project.mlxtran new file mode 100644 index 0000000..4af5eed --- /dev/null +++ b/inst/cov/warfarin_covariate3_project.mlxtran @@ -0,0 +1,89 @@ + + +[FILEINFO] +file='data/warfarin_data.csv' +delimiter = comma +header={id, time, amt, dv, dvid, wt, sex, age} + +[CONTENT] +id = {use=identifier} +time = {use=time} +amt = {use=amount} +dv = {use=observation, yname={'1', '2'}, type={continuous, continuous}} +dvid = {use=observationtype} +wt = {use=covariate, type=continuous} +sex = {use=covariate, type=categorical} + +[SETTINGS] +dataType = {'1'=plasma, '2'=plasma} + + + +[COVARIATE] +input = {wt, sex} + +sex = {type=categorical, categories={'0', '1'}} + +EQUATION: +lw70 = log(wt/70) + +DEFINITION: +tSex = +{ + transform = sex, + categories = { + 'F' = {'0'}, + 'M' = {'1'} }, + reference = 'M' +} + +[INDIVIDUAL] +input = {Tlag_pop, omega_Tlag, ka_pop, omega_ka, V_pop, omega_V, Cl_pop, omega_Cl, tSex, beta_V_tSex_F, beta_Cl_tSex_F} + +tSex = {type=categorical, categories={'F', 'M'}} + +DEFINITION: +Tlag = {distribution=logNormal, typical=Tlag_pop, sd=omega_Tlag} +ka = {distribution=logNormal, typical=ka_pop, sd=omega_ka} +V = {distribution=logNormal, typical=V_pop, covariate=tSex, coefficient={beta_V_tSex_F, 0}, sd=omega_V} +Cl = {distribution=logNormal, typical=Cl_pop, covariate=tSex, coefficient={beta_Cl_tSex_F, 0}, sd=omega_Cl} + +[LONGITUDINAL] +input = {a, b} + +file = 'lib:oral1_1cpt_TlagkaVCl.txt' + +DEFINITION: +concentration = {distribution=normal, prediction=Cc, errorModel=combined1(a, b)} + + +data = '1' +model = concentration + + +Cl_pop = {value=0.1, method=MLE} +Tlag_pop = {value=1, method=MLE} +V_pop = {value=5, method=MLE} +a = {value=1, method=MLE} +b = {value=0.3, method=MLE} +beta_Cl_tSex_F = {value=0, method=MLE} +beta_V_tSex_F = {value=0, method=MLE} +c = {value=1, method=FIXED} +ka_pop = {value=1, method=MLE} +omega_Cl = {value=1, method=MLE} +omega_Tlag = {value=1, method=MLE} +omega_V = {value=1, method=MLE} +omega_ka = {value=1, method=MLE} + + + +[TASKS] +populationParameters() +individualParameters(method = {conditionalMean, conditionalMode }) +fim(method = StochasticApproximation) +logLikelihood(method = ImportanceSampling) +plotResult(method = {indfits, parameterdistribution, covariancemodeldiagnosis, covariatemodeldiagnosis, obspred, vpc, residualsscatter, residualsdistribution, randomeffects, saemresults }) + +[SETTINGS] +GLOBAL: +exportpath = 'w3'