Part III - Chapter 7 |
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| warfarin_data.txt | the original warfarin PKPD data (only the PK data is used in this chapter) |
| warfarinPK_M0.mlxtran | Monolix project for model M0 used in Sections 7.1, 7.2 and 7.3 |
| warfarinPK_M1.mlxtran warfarinPK_M2b.mlxtran warfarinPK_M3b.mlxtran |
Monolix projects for models M1, M2 and M3 used in Section 7.3.4 ERRATUM: Results presented in the book with models M2 and M3 were obtained assuming a residual error model of the form y = f + a*e1+b*f*e2 , and not of the form y = f + (a+b*f)e as stated page 199 |
| warfarinPK_M2a.mlxtran warfarinPK_M3a.mlxtran |
Monolix projects for models M2 and M3 assuming a residual error model of the form y = f + (a+b*f)e |
| warfarinPK_Bayes1.mlxtran | Monolix project used Section 7.3.4, assuming that ka is fixed (ka=1) |
| warfarinPK_Bayes2a.mlxtran warfarinPK_Bayes2b.mlxtran warfarinPK_Bayes3a.mlxtran warfarinPK_Bayes3b.mlxtran warfarinPK_Bayes4a.mlxtran warfarinPK_Bayes4b.mlxtran warfarinPK_Bayes5a.mlxtran warfarinPK_Bayes5b.mlxtran |
Monolix projects used Section 7.3.4, assuming a log-normal prior for ka with standard deviation equal to 0.02 (2a and 2b), 0.04 (3a and 3b), 0.1 (4a and 4b) and 0.3 (5a and 5b).
The MAP estimate of ka is computed with projects 2a, 3a, 4a and 5a. The posterior distribution of ka is estimated with projects 2b, 3b, 4b and 5b. |
Part III - Chapter 8 |
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| ratMale.txt | the body weight data of the 80 males used in Section 8.1 |
| growth1_model.txt growth2_model.txt growth3_model.txt |
Growth models represented by equations (8.1), (8.3) and (8.4) |
| growth1_project.mlxtran growth2_project.mlxtran |
Monolix projects used in Section 8.1.2 |
| growth3_project.mlxtran growth4_project.mlxtran |
Monolix projects used in Section 8.1.3 |
| warfarin_data.txt | the original warfarin PKPD data used in Section 8.2.1 |
| pkpd1_mlxt.txt warfpkpd1_project.mlxtran |
Immediate response model and the Monolix project used Section 8.2.1.1 |
| pkpd2_mlxt.txt warfpkpd2_project.mlxtran |
Effect compartment model and the Monolix project used in Section 8.2.1.2 |
| pkpd3a_mlxt.txt pkpd3b_mlxt.txt warfpkpd3a_project.mlxtran warfpkpd3b_project.mlxtran |
Indirect response models and the Monolix projects used in Section 8.2.1.3 |
| warfpkpd4a_project.mlxtran | Monolix project used in Section 8.2.2 (sequential approach using estimated population PK parameters) |
| warfarin_seq_data.txt | the warfarin PKPD data used Section 8.2.2 for sequential PKPD modelling |
| pkpd4_mlxt.txt warfpkpd4b_project.mlxtran |
Indirect response model for sequential PKPD modelling and the Monolix project used Section 8.2.2 (sequential approach using estimated individual PK parameters) |
| warfarin_cat_data.txt | the warfarin PKPD data used in Section 8.2.3 for modelling categorical PD data |
| pkpd5_mlxt.txt warfpkpd5_project.mlxtran |
PKPD model for categorical PD data and the Monolix project used Section 8.2.3 |
| hog_data.csv | the florescence data used in Section 8.3 and displayed Figure 8.14 |
| hog1_mlxplore.txt | Mlxplore project used p 225 for visualizing the variables displayed Figure 8.15
ERRATUM: the script "reactionRate1_mlxplore.txt" is incomplete and should be replaced by "hog1_mlxplore.txt" |
| hog_modelMlxplore.txt | Hog1-induced gene expression model displayed page 226 as "reactionRate_mlxt.txt". This model is used by Mlxplore and Simulx. |
| hog2_mlxplore.txt | Mlxplore project displayed page 227 as "reactionRate2_mlxplore.txt" for visualizing the predicted fluorescence displayed Figure 8.16 |
| hog_modelMonolix.txt | Hog1-induced gene expression model used by Monolix. |
| hog1_monolix.mlxtran hog2_monolix.mlxtran |
Monolix projects used in Section 8.3 for modelling the fluorescence data stored in "hog_data.csv". |
| hog_simulx.R hog_simulx.m |
R and Matlab codes for simulating fluorescence data with Simulx from the reaction rate model implemented in "hog_modelMlxplore.txt". |
| hog_mlxplore.R hog_mlxplore.m |
R and Matlab codes for visualizing with Mlxplore the reaction rate model implemented in "hog_modelMlxplore.txt". |
Part III - Chapter 9 |
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| exsaem_data.csv | simulated data used in Section 9.2.4 |
| exsaem1_project.mlxtran exsaem2_project.mlxtran exsaem3_project.mlxtran exsaem4_project.mlxtran |
Monolix projects used in Section 9.2.4 |
| saem_animation1.m | Matlab code used in Section 9.2.5 |
| saem_animation2.m | additional Matlab code for visualizing the behavior of SAEM (not used in the book) |
| joint_data.csv | simulated data used in Section 9.2.6 |
| annealing1_project.mlxtran annealing2_project.mlxtran annealing3_project.mlxtran annealing4_project.mlxtran annealing5_project.mlxtran |
Monolix projects used in Section 9.2.6 |
| warfarin_data.txt | the warfarin data used in Section 9.3 |
| warfarinPK_project.mlxtran | Monolix project used in Section 9.3 |
| PKmixt_data.txt | simulated data used in Section 9.5 |
| ll1_project.mlxtran ll2_project.mlxtran ll3_project.mlxtran |
Monolix projects used in Section 9.5 |
| data1.csv data2.csv |
simulated data used Section 9.7 and displayed Figures 9.13 and 9.15 |
| binning1_project.mlxtran binning2_project.mlxtran |
Monolix projects used in Section 9.7 for producing the binnings displayed Figures 9.13 and 9.15 |
Appendix A |
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| individualFitting_data.txt | simulated data used Appendix A |
| individualFitting.R | R code used Appendix A |
Appendix C |
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| pk3_model.txt pk4_model.txt pk5_model.txt |
PK models 3, 4 and 5 displayed in Appendix C.4 |
| pk3_mlxplore.txt pk4a_mlxplore.txt pk4b_mlxplore.txt pk5_mlxplore.txt |
Mlxplore scripts used for visualizing Models 3, 4 and 5 (only Model 5 is presented in Appendix C.4 under the name "pk_model.txt") |
| pk3_simulx.m pk3_simulx.R pk4a_simulx.m pk4a_simulx.R pk4b_simulx.m pk4b_simulx.R pk5_simulx.m pk5_simulx.R |
R and Matlab codes for simulating Models 3, 4 and 5 using Simulx (only Model 5 is presented in Appendix C.4) |
| pk3_mlxplore.m pk3_mlxplore.R pk4a_mlxplore.m pk4a_mlxplore.R pk4b_mlxplore.m pk4b_mlxplore.R pk5_mlxplore.m pk5_mlxplore.R |
R and Matlab codes for visualizing Models 3, 4 and 5 using Mlxplore (these examples are not used in the book) |
Appendix D |
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| tumor1_model.txt tumor2_model.txt |
tumor growth models used in Appendix D.1 with Mlxplore and Appendix D.2 with Simulx |
| tumor1a_mlxplore.txt tumor1b_mlxplore.txt tumor2_mlxplore.txt |
Mlxplore projects used in Appendix D.1 |
| tumor3_model.txt | tumor growth model used in Appendix D.2 with Simulx |
| tumor1a_simulx.R tumor1a_simulx.m tumor1b_simulx.R tumor1b_simulx.m tumor2_simulx.R tumor2_simulx.m tumor3_simulx.R tumor3_simulx.m |
R and Matlab codes used in Appendix D.2 for simulating tumor growth data with Simulx |
| warfarin_data.txt pkrtte_data.txt |
warfarin data and time-to-event data used in Appendix D.3 with Datxplore |
| warfarin_datxplore.txt pkrtte_datxplore.txt |
Datxplore projects used in Appendix D.3 |