Nothing
tests/testthat/_snaps/builtin_mapping.md
In Certara.RsNLME: Pharmacometric Modeling
Mapping for built-in models works
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : pkmodel",
"Is population : TRUE",
"Model Type : PK",
"",
" PK ",
" ------------------------------------------- ",
"Parameterization : Clearance",
"Absorption : Intravenous",
"Num Compartments : 3",
"Dose Tlag? : FALSE",
"Elimination Comp ?: FALSE",
"Infusion Allowed ?: FALSE",
"Sequential : FALSE",
"Freeze PK : FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" cfMicro(A1,Cl/V, Cl2/V, Cl2/V2, Cl3/V, Cl3/V3)",
" dosepoint(A1)",
" C = A1 / V",
" error(CEps=0.1)",
" observe(CObs=C * ( 1 + CEps))",
" stparm(V = tvV * exp(nV))",
" stparm(Cl = tvCl * exp(nCl))",
" stparm(V2 = tvV2 * exp(nV2))",
" stparm(Cl2 = tvCl2 * exp(nCl2))",
" stparm(V3 = tvV3 * exp(nV3))",
" stparm(Cl3 = tvCl3 * exp(nCl3))",
" fixef( tvV = c(,1,))",
" fixef( tvCl = c(,1,))",
" fixef( tvV2 = c(,1,))",
" fixef( tvCl2 = c(,1,))",
" fixef( tvV3 = c(,1,))",
" fixef( tvCl3 = c(,1,))",
" ranef(diag(nV,nCl,nV2,nCl2,nV3,nCl3) = c(1,1,1,1,1,1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" V Cl V2 Cl2 V3 Cl3",
" ------------------------------------------- ",
"Observations:",
"Observation Name : CObs",
"Effect Name : C",
"Epsilon Name : CEps",
"Epsilon Type : Multiplicative",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : Subject,ID2",
"time : Act_Time",
"A1 : Amount",
"CObs : Conc",
""
]
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : linearmodel",
"Is population : TRUE",
"Model Type : LINEAR",
"",
" Linear ",
" ------------------------------------------- ",
"Linear Type : E = EAlpha + EBeta*C ",
"Linear Frozen : FALSE",
"Effect Compartment: FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" covariate(C)",
" E = EAlpha + EBeta*C",
" error(EEps=1)",
" observe(EObs(C)=E + EEps)",
" stparm(EAlpha = tvEAlpha * exp(nEAlpha))",
" stparm(EBeta = tvEBeta * exp(nEBeta))",
" fixef( tvEAlpha = c(,1,))",
" fixef( tvEBeta = c(,1,))",
" ranef(diag(nEAlpha,nEBeta) = c(1,1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" EAlpha EBeta",
" ------------------------------------------- ",
"Observations:",
"Observation Name : EObs",
"Effect Name : E",
"Epsilon Name : EEps",
"Epsilon Type : Additive",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : ID",
"C : CObs",
"EObs : EObs",
""
]
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : emaxmodel",
"Is population : TRUE",
"Model Type : EMAX",
"",
" PD ",
" ------------------------------------------- ",
"Check Baseline : TRUE",
"Check Inhibitory : TRUE",
"Check Sigmoid : FALSE",
"Check Fractional : TRUE",
"Effect Compartment: FALSE",
"Freeze PD : FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" covariate(C)",
" E = E0 * (1 - Imax * C / (IC50 + C))",
" error(EEps=1)",
" observe(EObs(C)=E + EEps)",
" stparm(IC50 = tvIC50 * exp(nIC50))",
" stparm(E0 = tvE0 * exp(nE0))",
" stparm(Imax = tvImax * exp(nImax))",
" fixef( tvIC50 = c(,1,))",
" fixef( tvE0 = c(,1,))",
" fixef( tvImax = c(,1,))",
" ranef(diag(nIC50,nE0,nImax) = c(1,1,1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" IC50 E0 Imax",
" ------------------------------------------- ",
"Observations:",
"Observation Name : EObs",
"Effect Name : E",
"Epsilon Name : EEps",
"Epsilon Type : Additive",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : ID",
"C : CObs",
"EObs : EObs",
""
]
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : pklinearmodel",
"Is population : TRUE",
"Model Type : PK_LINEAR",
"",
" PK ",
" ------------------------------------------- ",
"Parameterization : Micro",
"Absorption : Intravenous",
"Num Compartments : 1",
"Dose Tlag? : FALSE",
"Elimination Comp ?: FALSE",
"Infusion Allowed ?: FALSE",
"Sequential : TRUE",
"Freeze PK : FALSE",
"",
" Linear ",
" ------------------------------------------- ",
"Linear Type : E = EAlpha ",
"Linear Frozen : FALSE",
"Effect Compartment: FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" cfMicro(A1, Ke)",
" dosepoint(A1)",
" C = A1 / V",
" E = EAlpha",
" error(EEps=1)",
" observe(EObs=E + EEps)",
" stparm(V = tvV * exp(nV))",
" stparm(Ke = tvKe * exp(nKe))",
" stparm(EAlpha = tvEAlpha * exp(nEAlpha))",
" fixef( tvV(freeze) = c(,1,))",
" fixef( tvKe(freeze) = c(,1,))",
" fixef( tvEAlpha = c(,1,))",
" covariate(nV,nKe)",
" ranef(diag(nEAlpha) = c(1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" V Ke EAlpha",
" ------------------------------------------- ",
"Observations:",
"Observation Name : EObs",
"Effect Name : E",
"Epsilon Name : EEps",
"Epsilon Type : Additive",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : ID",
"time : Time",
"A1 : Dose",
"EObs : EObs",
"nV : nV",
"nKe : nKe",
""
]
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : Sequential",
"Is population : TRUE",
"Model Type : PK_EMAX",
"",
" PK ",
" ------------------------------------------- ",
"Parameterization : Micro",
"Absorption : Gamma",
"Num Compartments : 3",
"Dose Tlag? : FALSE",
"Elimination Comp ?: TRUE",
"Fraction Excreted : FALSE",
"Infusion Allowed ?: FALSE",
"Sequential : TRUE",
"Freeze PK : FALSE",
"",
" PD ",
" ------------------------------------------- ",
"Check Baseline : TRUE",
"Check Inhibitory : TRUE",
"Check Sigmoid : TRUE",
"Check Fractional : TRUE",
"Effect Compartment: FALSE",
"Freeze PD : FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" dosepoint(A1)",
" C = A1 / V",
" delayInfCpt(A1, MeanDelayTime, ShapeParamMinusOne, out = - Ke * A1 - K12 * A1 + K21 * A2 - K13 * A1 + K31 * A3, dist = Gamma)",
" deriv(A2 = K12 * A1 - K21 * A2)",
" deriv(A3 = K13 * A1 - K31 * A3)",
" urinecpt(A0 = Ke * A1)",
" E = E0 * (1 - Imax * C^Gam / (IC50^Gam + C^Gam))",
" error(A0Eps(freeze)=0.1)",
" observe(A0Obs=A0 * ( 1 + A0Eps))",
" error(EEps=1)",
" observe(EObs=E + EEps)",
" stparm(MeanDelayTime = tvMeanDelayTime * exp(nMeanDelayTime))",
" stparm(ShapeParamMinusOne = tvShapeParamMinusOne * exp(nShapeParamMinusOne))",
" stparm(V = tvV * exp(nV))",
" stparm(Ke = tvKe * exp(nKe))",
" stparm(K12 = tvK12 * exp(nK12))",
" stparm(K21 = tvK21 * exp(nK21))",
" stparm(K13 = tvK13 * exp(nK13))",
" stparm(K31 = tvK31 * exp(nK31))",
" stparm(IC50 = tvIC50 * exp(nIC50))",
" stparm(Gam = tvGam * exp(nGam))",
" stparm(E0 = tvE0 * exp(nE0))",
" stparm(Imax = tvImax * exp(nImax))",
" fixef( tvMeanDelayTime(freeze) = c(,1,))",
" fixef( tvShapeParamMinusOne(freeze) = c(,1,))",
" fixef( tvV(freeze) = c(,1,))",
" fixef( tvKe(freeze) = c(,1,))",
" fixef( tvK12(freeze) = c(,1,))",
" fixef( tvK21(freeze) = c(,1,))",
" fixef( tvK13(freeze) = c(,1,))",
" fixef( tvK31(freeze) = c(,1,))",
" fixef( tvIC50 = c(,1,))",
" fixef( tvGam = c(,1,))",
" fixef( tvE0 = c(,1,))",
" fixef( tvImax = c(,1,))",
" covariate(nMeanDelayTime,nShapeParamMinusOne,nV,nKe,nK12,nK21,nK13,nK31)",
" ranef(diag(nIC50,nGam,nE0,nImax) = c(1,1,1,1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" MeanDelayTime ShapeParamMinusOne V Ke K12 K21 K13 K31 IC50 Gam E0 Imax",
" ------------------------------------------- ",
"Observations:",
"Observation Name : A0Obs",
"Effect Name : A0",
"Epsilon Name : A0Eps",
"Epsilon Type : Multiplicative",
"Epsilon frozen : TRUE",
"is BQL : FALSE",
" ------------------------------------------- ",
"Observation Name : EObs",
"Effect Name : E",
"Epsilon Name : EEps",
"Epsilon Type : Additive",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : Subject",
"time : Nom_Time",
"A1 : Amount",
"A0Obs : Gender",
"EObs : Age",
"nMeanDelayTime : nMeanDelayTime",
"nShapeParamMinusOne : nShapeParamMinusOne",
"nV : nV",
"nKe : nKe",
"nK12 : nK12",
"nK21 : nK21",
"nK13 : nK13",
"nK31 : nK31",
""
]
Try the Certara.RsNLME package in your browser
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Certara.RsNLME documentation built on April 3, 2025, 11:04 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Mapping for built-in models works
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : pkmodel",
"Is population : TRUE",
"Model Type : PK",
"",
" PK ",
" ------------------------------------------- ",
"Parameterization : Clearance",
"Absorption : Intravenous",
"Num Compartments : 3",
"Dose Tlag? : FALSE",
"Elimination Comp ?: FALSE",
"Infusion Allowed ?: FALSE",
"Sequential : FALSE",
"Freeze PK : FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" cfMicro(A1,Cl/V, Cl2/V, Cl2/V2, Cl3/V, Cl3/V3)",
" dosepoint(A1)",
" C = A1 / V",
" error(CEps=0.1)",
" observe(CObs=C * ( 1 + CEps))",
" stparm(V = tvV * exp(nV))",
" stparm(Cl = tvCl * exp(nCl))",
" stparm(V2 = tvV2 * exp(nV2))",
" stparm(Cl2 = tvCl2 * exp(nCl2))",
" stparm(V3 = tvV3 * exp(nV3))",
" stparm(Cl3 = tvCl3 * exp(nCl3))",
" fixef( tvV = c(,1,))",
" fixef( tvCl = c(,1,))",
" fixef( tvV2 = c(,1,))",
" fixef( tvCl2 = c(,1,))",
" fixef( tvV3 = c(,1,))",
" fixef( tvCl3 = c(,1,))",
" ranef(diag(nV,nCl,nV2,nCl2,nV3,nCl3) = c(1,1,1,1,1,1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" V Cl V2 Cl2 V3 Cl3",
" ------------------------------------------- ",
"Observations:",
"Observation Name : CObs",
"Effect Name : C",
"Epsilon Name : CEps",
"Epsilon Type : Multiplicative",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : Subject,ID2",
"time : Act_Time",
"A1 : Amount",
"CObs : Conc",
""
]
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : linearmodel",
"Is population : TRUE",
"Model Type : LINEAR",
"",
" Linear ",
" ------------------------------------------- ",
"Linear Type : E = EAlpha + EBeta*C ",
"Linear Frozen : FALSE",
"Effect Compartment: FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" covariate(C)",
" E = EAlpha + EBeta*C",
" error(EEps=1)",
" observe(EObs(C)=E + EEps)",
" stparm(EAlpha = tvEAlpha * exp(nEAlpha))",
" stparm(EBeta = tvEBeta * exp(nEBeta))",
" fixef( tvEAlpha = c(,1,))",
" fixef( tvEBeta = c(,1,))",
" ranef(diag(nEAlpha,nEBeta) = c(1,1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" EAlpha EBeta",
" ------------------------------------------- ",
"Observations:",
"Observation Name : EObs",
"Effect Name : E",
"Epsilon Name : EEps",
"Epsilon Type : Additive",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : ID",
"C : CObs",
"EObs : EObs",
""
]
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : emaxmodel",
"Is population : TRUE",
"Model Type : EMAX",
"",
" PD ",
" ------------------------------------------- ",
"Check Baseline : TRUE",
"Check Inhibitory : TRUE",
"Check Sigmoid : FALSE",
"Check Fractional : TRUE",
"Effect Compartment: FALSE",
"Freeze PD : FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" covariate(C)",
" E = E0 * (1 - Imax * C / (IC50 + C))",
" error(EEps=1)",
" observe(EObs(C)=E + EEps)",
" stparm(IC50 = tvIC50 * exp(nIC50))",
" stparm(E0 = tvE0 * exp(nE0))",
" stparm(Imax = tvImax * exp(nImax))",
" fixef( tvIC50 = c(,1,))",
" fixef( tvE0 = c(,1,))",
" fixef( tvImax = c(,1,))",
" ranef(diag(nIC50,nE0,nImax) = c(1,1,1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" IC50 E0 Imax",
" ------------------------------------------- ",
"Observations:",
"Observation Name : EObs",
"Effect Name : E",
"Epsilon Name : EEps",
"Epsilon Type : Additive",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : ID",
"C : CObs",
"EObs : EObs",
""
]
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : pklinearmodel",
"Is population : TRUE",
"Model Type : PK_LINEAR",
"",
" PK ",
" ------------------------------------------- ",
"Parameterization : Micro",
"Absorption : Intravenous",
"Num Compartments : 1",
"Dose Tlag? : FALSE",
"Elimination Comp ?: FALSE",
"Infusion Allowed ?: FALSE",
"Sequential : TRUE",
"Freeze PK : FALSE",
"",
" Linear ",
" ------------------------------------------- ",
"Linear Type : E = EAlpha ",
"Linear Frozen : FALSE",
"Effect Compartment: FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" cfMicro(A1, Ke)",
" dosepoint(A1)",
" C = A1 / V",
" E = EAlpha",
" error(EEps=1)",
" observe(EObs=E + EEps)",
" stparm(V = tvV * exp(nV))",
" stparm(Ke = tvKe * exp(nKe))",
" stparm(EAlpha = tvEAlpha * exp(nEAlpha))",
" fixef( tvV(freeze) = c(,1,))",
" fixef( tvKe(freeze) = c(,1,))",
" fixef( tvEAlpha = c(,1,))",
" covariate(nV,nKe)",
" ranef(diag(nEAlpha) = c(1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" V Ke EAlpha",
" ------------------------------------------- ",
"Observations:",
"Observation Name : EObs",
"Effect Name : E",
"Epsilon Name : EEps",
"Epsilon Type : Additive",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : ID",
"time : Time",
"A1 : Dose",
"EObs : EObs",
"nV : nV",
"nKe : nKe",
""
]
[
"",
" Model Overview ",
" ------------------------------------------- ",
"Model Name : Sequential",
"Is population : TRUE",
"Model Type : PK_EMAX",
"",
" PK ",
" ------------------------------------------- ",
"Parameterization : Micro",
"Absorption : Gamma",
"Num Compartments : 3",
"Dose Tlag? : FALSE",
"Elimination Comp ?: TRUE",
"Fraction Excreted : FALSE",
"Infusion Allowed ?: FALSE",
"Sequential : TRUE",
"Freeze PK : FALSE",
"",
" PD ",
" ------------------------------------------- ",
"Check Baseline : TRUE",
"Check Inhibitory : TRUE",
"Check Sigmoid : TRUE",
"Check Fractional : TRUE",
"Effect Compartment: FALSE",
"Freeze PD : FALSE",
"",
" PML ",
" ------------------------------------------- ",
"test(){",
" dosepoint(A1)",
" C = A1 / V",
" delayInfCpt(A1, MeanDelayTime, ShapeParamMinusOne, out = - Ke * A1 - K12 * A1 + K21 * A2 - K13 * A1 + K31 * A3, dist = Gamma)",
" deriv(A2 = K12 * A1 - K21 * A2)",
" deriv(A3 = K13 * A1 - K31 * A3)",
" urinecpt(A0 = Ke * A1)",
" E = E0 * (1 - Imax * C^Gam / (IC50^Gam + C^Gam))",
" error(A0Eps(freeze)=0.1)",
" observe(A0Obs=A0 * ( 1 + A0Eps))",
" error(EEps=1)",
" observe(EObs=E + EEps)",
" stparm(MeanDelayTime = tvMeanDelayTime * exp(nMeanDelayTime))",
" stparm(ShapeParamMinusOne = tvShapeParamMinusOne * exp(nShapeParamMinusOne))",
" stparm(V = tvV * exp(nV))",
" stparm(Ke = tvKe * exp(nKe))",
" stparm(K12 = tvK12 * exp(nK12))",
" stparm(K21 = tvK21 * exp(nK21))",
" stparm(K13 = tvK13 * exp(nK13))",
" stparm(K31 = tvK31 * exp(nK31))",
" stparm(IC50 = tvIC50 * exp(nIC50))",
" stparm(Gam = tvGam * exp(nGam))",
" stparm(E0 = tvE0 * exp(nE0))",
" stparm(Imax = tvImax * exp(nImax))",
" fixef( tvMeanDelayTime(freeze) = c(,1,))",
" fixef( tvShapeParamMinusOne(freeze) = c(,1,))",
" fixef( tvV(freeze) = c(,1,))",
" fixef( tvKe(freeze) = c(,1,))",
" fixef( tvK12(freeze) = c(,1,))",
" fixef( tvK21(freeze) = c(,1,))",
" fixef( tvK13(freeze) = c(,1,))",
" fixef( tvK31(freeze) = c(,1,))",
" fixef( tvIC50 = c(,1,))",
" fixef( tvGam = c(,1,))",
" fixef( tvE0 = c(,1,))",
" fixef( tvImax = c(,1,))",
" covariate(nMeanDelayTime,nShapeParamMinusOne,nV,nKe,nK12,nK21,nK13,nK31)",
" ranef(diag(nIC50,nGam,nE0,nImax) = c(1,1,1,1))",
"}",
"",
" Structural Parameters ",
" ------------------------------------------- ",
" MeanDelayTime ShapeParamMinusOne V Ke K12 K21 K13 K31 IC50 Gam E0 Imax",
" ------------------------------------------- ",
"Observations:",
"Observation Name : A0Obs",
"Effect Name : A0",
"Epsilon Name : A0Eps",
"Epsilon Type : Multiplicative",
"Epsilon frozen : TRUE",
"is BQL : FALSE",
" ------------------------------------------- ",
"Observation Name : EObs",
"Effect Name : E",
"Epsilon Name : EEps",
"Epsilon Type : Additive",
"Epsilon frozen : FALSE",
"is BQL : FALSE",
" ------------------------------------------- ",
" Column Mappings ",
" ------------------------------------------- ",
"Model Variable Name : Data Column name",
"id : Subject",
"time : Nom_Time",
"A1 : Amount",
"A0Obs : Gender",
"EObs : Age",
"nMeanDelayTime : nMeanDelayTime",
"nShapeParamMinusOne : nShapeParamMinusOne",
"nV : nV",
"nKe : nKe",
"nK12 : nK12",
"nK21 : nK21",
"nK13 : nK13",
"nK31 : nK31",
""
]
Try the Certara.RsNLME package in your browser
Any scripts or data that you put into this service are public.
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