# Modelling and Simulation **URL:** https://forum.certara.com/c/phoenix/certara-forums/modelling-and-simulation/27.md [Latest](https://forum.certara.com/latest.md) · [Categories](https://forum.certara.com/categories.md) · [Tags](https://forum.certara.com/tags.md) --- ## [About the Modelling and Simulation category](https://forum.certara.com/t/about-the-modelling-and-simulation-category/4124)
**Author:** [@system](https://forum.certara.com/u/system)\ **Replies:** 0\ **Last updated:** [March 24, 2025, 2:28am UTC](https://forum.certara.com/t/about-the-modelling-and-simulation-category/4124 "2025-03-24T02:28:54Z")
--- ## [Covariate exploration in crossover model](https://forum.certara.com/t/covariate-exploration-in-crossover-model/4413)
**Author:** [@Bruno\_Pypendop](https://forum.certara.com/u/Bruno_Pypendop)\ **Replies:** 6\ **Last updated:** [August 4, 2026, 10:04pm UTC](https://forum.certara.com/t/covariate-exploration-in-crossover-model/4413 "2026-08-04T22:04:24Z")
I have a PK model for which I would like to include a period (occasion) effect then explore whether a categorical covariate may also have an effect. There is overlap since the categorical covariate is related to the admi… --- ## [PK-PD model of Binary repsonse](https://forum.certara.com/t/pk-pd-model-of-binary-repsonse/3630)
**Author:** [@ygsla](https://forum.certara.com/u/ygsla)\ **Replies:** 5\ **Last updated:** [April 20, 2026, 8:42pm UTC](https://forum.certara.com/t/pk-pd-model-of-binary-repsonse/3630 "2026-04-20T20:42:47Z")
HI Folks, Can we develop PK-PD model with binary reponse data in NLME? If yes, sharing some more information or suggestion or any built template will be appreciated. Thanks in advance!! Regards, Ygs --- ## [Using observed baselines values as fixed parameter value](https://forum.certara.com/t/using-observed-baselines-values-as-fixed-parameter-value/3723)
**Author:** [@cmukashyaka](https://forum.certara.com/u/cmukashyaka)\ **Replies:** 2\ **Last updated:** [March 6, 2026, 5:15pm UTC](https://forum.certara.com/t/using-observed-baselines-values-as-fixed-parameter-value/3723 "2026-03-06T17:15:07Z")
Hello, I am working on an indirect response model (limited inhibition of Kin), I have baseline values for each subject measured at the start of study. I need to use these values and fix them as E0 where E0 = Kin/Kout so… --- ## [Efficiently Calculating Cmax and AUC with 95% CI for 5th, 50th, and 95th Quartiles in Large Phoenix NLME Simulations](https://forum.certara.com/t/efficiently-calculating-cmax-and-auc-with-95-ci-for-5th-50th-and-95th-quartiles-in-large-phoenix-nlme-simulations/4357)
**Author:** [@Bhim\_Bahadur](https://forum.certara.com/u/Bhim_Bahadur)\ **Replies:** 5\ **Last updated:** [January 20, 2026, 9:00pm UTC](https://forum.certara.com/t/efficiently-calculating-cmax-and-auc-with-95-ci-for-5th-50th-and-95th-quartiles-in-large-phoenix-nlme-simulations/4357 "2026-01-20T21:00:43Z")
Hi Users and Experts, I used Phoenix NLME to simulate concentration–time (CT) profiles for 56 subjects with 1000 replicates each, over 672 hours with 1‑hour sampling. This produced a dataset of ~37 million rows. Phoenix… --- ## [Question regarding Parameter Freezing for Simulation: Should I fix both Fixed and Random Effects?](https://forum.certara.com/t/question-regarding-parameter-freezing-for-simulation-should-i-fix-both-fixed-and-random-effects/4353)
**Author:** [@Virunya\_Komenkul](https://forum.certara.com/u/Virunya_Komenkul)\ **Replies:** 2\ **Last updated:** [January 20, 2026, 7:48am UTC](https://forum.certara.com/t/question-regarding-parameter-freezing-for-simulation-should-i-fix-both-fixed-and-random-effects/4353 "2026-01-20T07:48:01Z")
Hi everyone, I am currently working on a simulation step using my final PK/PD model in Phoenix NLME. I have a question regarding the best practice for “freezing” parameters before running the simulation. When transitio… --- ## [Phoenix NLME simulation issue](https://forum.certara.com/t/phoenix-nlme-simulation-issue/4355)
**Author:** [@sylim](https://forum.certara.com/u/sylim)\ **Replies:** 6\ **Last updated:** [January 9, 2026, 8:48pm UTC](https://forum.certara.com/t/phoenix-nlme-simulation-issue/4355 "2026-01-09T20:48:01Z")
Hi, I added two simulation tables in Phoenix NLME. Table 01 uses continuous time points: seq(0,336,0.5), Table 02 uses specific time points at 310, 312, 314, etc. The simulated concentrations in Table 01 and Table 02 we… --- ## [Allometric scaling animal to human](https://forum.certara.com/t/allometric-scaling-animal-to-human/3412)
**Author:** [@harishkaushik](https://forum.certara.com/u/harishkaushik)\ **Replies:** 2\ **Last updated:** [December 16, 2025, 5:56pm UTC](https://forum.certara.com/t/allometric-scaling-animal-to-human/3412 "2025-12-16T17:56:46Z")
Hello, I have preclinical PK data from 4 species (Mice,Rat,GuineaPig & Dog) i wanted to utilise the phoenix automation for predicting FIH dose and profile, I viewed the webinar by Serge it was helpful, but is there any… --- ## [Mixture Models with latent covariate with NLME](https://forum.certara.com/t/mixture-models-with-latent-covariate-with-nlme/4339)
**Author:** [@phychadelicpk](https://forum.certara.com/u/phychadelicpk)\ **Replies:** 1\ **Last updated:** [October 24, 2025, 6:13pm UTC](https://forum.certara.com/t/mixture-models-with-latent-covariate-with-nlme/4339 "2025-10-24T18:13:45Z")
Hi all, I am looking to reproduce a model that college developed in Monolix. They used a mixture model with a latent covariate. In my search of the manual, I see no ability to do this in NLME. I saw this confirmed by a … --- ## [Multiple oral dose population PK model](https://forum.certara.com/t/multiple-oral-dose-population-pk-model/4336)
**Author:** [@sabdulm1](https://forum.certara.com/u/sabdulm1)\ **Replies:** 2\ **Last updated:** [October 21, 2025, 4:46pm UTC](https://forum.certara.com/t/multiple-oral-dose-population-pk-model/4336 "2025-10-21T16:46:37Z")
Hello, I have a PK model for a drug that is dosed once a day for three days. I have modeled the first dose well with an enterohepatic recirculation model. I want to try adding the other two doses now. I have in my origi… --- ## [How to appropriately cite Phoenix products](https://forum.certara.com/t/how-to-appropriately-cite-phoenix-products/2804)
**Author:** [@vivaturi](https://forum.certara.com/u/vivaturi)\ **Replies:** 7\ **Last updated:** [August 29, 2025, 8:09am UTC](https://forum.certara.com/t/how-to-appropriately-cite-phoenix-products/2804 "2025-08-29T08:09:53Z")
Can someone provide a standard way to cite the use Phoenix in reports/publications etc. Is it different for citing NLME vs NCA vs IVIVC etc.. Thanks Vijay --- ## [Changing Output units for V and Cl](https://forum.certara.com/t/changing-output-units-for-v-and-cl/2295)
**Author:** [@jmcdowell](https://forum.certara.com/u/jmcdowell)\ **Replies:** 7\ **Last updated:** [July 18, 2025, 9:20pm UTC](https://forum.certara.com/t/changing-output-units-for-v-and-cl/2295 "2025-07-18T21:20:18Z")
Dear All, this seems like such a silly question but I can’t seem to find the answer in any documentation. My input is conc in ng/mL and time is in minutes so I’m getting V in mL and Cl in mL/min. However, I desire the re… --- ## [Modeling between period variation](https://forum.certara.com/t/modeling-between-period-variation/4274)
**Author:** [@phychadelicpk](https://forum.certara.com/u/phychadelicpk)\ **Replies:** 5\ **Last updated:** [July 3, 2025, 9:39pm UTC](https://forum.certara.com/t/modeling-between-period-variation/4274 "2025-07-03T21:39:30Z")
Hi all, I got a bunch of studies, that include MAD and cross over studies of different dose levels. Just looking at the plots there appears to be cyp induction that you would only see in the more drawn out studies. I as… --- ## [Zero-order absorption 2-compartment model](https://forum.certara.com/t/zero-order-absorption-2-compartment-model/4229)
**Author:** [@weizixu0110](https://forum.certara.com/u/weizixu0110)\ **Replies:** 3\ **Last updated:** [June 2, 2025, 4:13pm UTC](https://forum.certara.com/t/zero-order-absorption-2-compartment-model/4229 "2025-06-02T16:13:35Z")
Hi, I’m trying to build a 2-compartment model with zero-order absorption. Based on other posts, I started with a 2-compartment IV model, then modified it to include zero-order absorption by adding Tabs for duration. I’m… --- ## [Transit compartment + Michaelis Menten absorption](https://forum.certara.com/t/transit-compartment-michaelis-menten-absorption/4220)
**Author:** [@Juliette\_Monbrun](https://forum.certara.com/u/Juliette_Monbrun)\ **Replies:** 3\ **Last updated:** [May 27, 2025, 6:38am UTC](https://forum.certara.com/t/transit-compartment-michaelis-menten-absorption/4220 "2025-05-27T06:38:50Z")
Dear All, I am building a pharmacokinetic population model after oral administrations. I tried several absorption model with Tlags and Michaelis Menten absorption with Tlag which has the better fitting. Now I am trying … --- ## [NLME myelosuppression model](https://forum.certara.com/t/nlme-myelosuppression-model/2726)
**Author:** [@rdfbeaner](https://forum.certara.com/u/rdfbeaner)\ **Replies:** 5\ **Last updated:** [May 22, 2025, 5:49pm UTC](https://forum.certara.com/t/nlme-myelosuppression-model/2726 "2025-05-22T17:49:24Z")
Working within NLME to implement a semi-mechanistic PK/PD model to describe the chemotherapy induced myelosuppression of various chemotherapeutics. Interested in using the PK/PD myelosuppression model described by Friber… --- ## [Implement Residua Unexplained Variability in a Population PK Model](https://forum.certara.com/t/implement-residua-unexplained-variability-in-a-population-pk-model/4168)
**Author:** [@david\_2](https://forum.certara.com/u/david_2)\ **Replies:** 2\ **Last updated:** [April 15, 2025, 1:41pm UTC](https://forum.certara.com/t/implement-residua-unexplained-variability-in-a-population-pk-model/4168 "2025-04-15T13:41:12Z")
I am conducting a model-based simulation using PK parameters from a publication. The publication reports(table): I attempted to include StudyA as a covariate, but not sure if I am doing right. I would greatly appreci… --- ## [VPC line broken](https://forum.certara.com/t/vpc-line-broken/3756)
**Author:** [@estherwinter](https://forum.certara.com/u/estherwinter)\ **Replies:** 3\ **Last updated:** [March 21, 2025, 9:26am UTC](https://forum.certara.com/t/vpc-line-broken/3756 "2025-03-21T09:26:48Z")
Hello, Can anyone explain to me why the 5% line of the predicted quantile is broken in the VPC? See attached VPC graph. It concerns a dataset of sparse sampling and multiple administrations (in some subjects). Hope som… --- ## [Reproducing published model](https://forum.certara.com/t/reproducing-published-model/3753)
**Author:** [@Helmut\_Schuetz](https://forum.certara.com/u/Helmut_Schuetz)\ **Replies:** 1\ **Last updated:** [November 15, 2024, 4:04pm UTC](https://forum.certara.com/t/reproducing-published-model/3753 "2024-11-15T16:04:11Z")
I tried to reproduce the model of Gupta et.al. (https://doi.org/10.1007/s40262-017-0526-4) in simulations. Only the structural model and I dropped the irrelevant lag-time. I had to interrupt the sim’s because no results … --- ## [Lack of CV% in Theta page](https://forum.certara.com/t/lack-of-cv-in-theta-page/3749)
**Author:** [@peggy.lin](https://forum.certara.com/u/peggy.lin)\ **Replies:** 2\ **Last updated:** [October 9, 2024, 7:57pm UTC](https://forum.certara.com/t/lack-of-cv-in-theta-page/3749 "2024-10-09T19:57:15Z")
Hi all, I have rat PK data for 4 formulations. One of the formulation (group 2) is the fast-releasing patch. I used the mean concentration from group 2 animals for PK modeling. I ran the model with good fitting and diag… --- ## [Deconvolution Results: Interpretation When Considering Low Bioavailability](https://forum.certara.com/t/deconvolution-results-interpretation-when-considering-low-bioavailability/3743)
**Author:** [@danielcoliveira4](https://forum.certara.com/u/danielcoliveira4)\ **Replies:** 1\ **Last updated:** [March 22, 2024, 9:08am UTC](https://forum.certara.com/t/deconvolution-results-interpretation-when-considering-low-bioavailability/3743 "2024-03-22T09:08:03Z")
Hello, I performed a deconvolution to obtain the release rate of a long-acting implant by inputting the unit impulse response of the IV formulation of the drug alongside mapping the subcutaneous conc v time profiles. I’… --- ## [covariate](https://forum.certara.com/t/covariate/3746)
**Author:** [@linda](https://forum.certara.com/u/linda)\ **Replies:** 1\ **Last updated:** [March 21, 2024, 10:14pm UTC](https://forum.certara.com/t/covariate/3746 "2024-03-21T22:14:14Z")
Hi all, What method does Phoenix use to assess significance of covariate relationships with PK parameters in pop PK model? After I add a binary categorical covariate to the model. In the result tab, I can get a box… --- ## [small STDERR and CV%](https://forum.certara.com/t/small-stderr-and-cv/3738)
**Author:** [@liuxiaolin](https://forum.certara.com/u/liuxiaolin)\ **Replies:** 3\ **Last updated:** [March 16, 2024, 9:19am UTC](https://forum.certara.com/t/small-stderr-and-cv/3738 "2024-03-16T09:19:34Z")
Hi all, I’ve gained really small stderr and CV% when using QRPEM algorithm, attached below. Does it a true value? If not, is it possible to solve this problem? Besides, I’ve tried FOCE-ELS with sandwich method, but th… --- ## [large shrinkage when CObs is limited](https://forum.certara.com/t/large-shrinkage-when-cobs-is-limited/3741)
**Author:** [@liuxiaolin](https://forum.certara.com/u/liuxiaolin)\ **Replies:** 1\ **Last updated:** [March 1, 2024, 6:45am UTC](https://forum.certara.com/t/large-shrinkage-when-cobs-is-limited/3741 "2024-03-01T06:45:39Z")
Hi all, I have data from 3 studies. Study 202 and 203 got abundant sampling PK data (0, 0.5, 1, 2, 4, 6, 8, 12, 24 hr after dose), while Study206 had only sparse sampling (0, 1.5 hr) . When I used only data from 202 an… --- ## [simulation of concentrations from two compartments](https://forum.certara.com/t/simulation-of-concentrations-from-two-compartments/3739)
**Author:** [@mjpk](https://forum.certara.com/u/mjpk)\ **Replies:** 7\ **Last updated:** [February 28, 2024, 7:07pm UTC](https://forum.certara.com/t/simulation-of-concentrations-from-two-compartments/3739 "2024-02-28T19:07:42Z")
Hi I have a fitted model that I would like to try alternative dosing schemes. My problem is I have two compartments that I wish to simulate in the same model. My model was made in text mode and I have to obs variables i… --- ## [Questions about plots CWRES-IVAR and CWRES-TAD](https://forum.certara.com/t/questions-about-plots-cwres-ivar-and-cwres-tad/3737)
**Author:** [@zzzz](https://forum.certara.com/u/zzzz)\ **Replies:** 6\ **Last updated:** [February 26, 2024, 11:54am UTC](https://forum.certara.com/t/questions-about-plots-cwres-ivar-and-cwres-tad/3737 "2024-02-26T11:54:45Z")
Dear all， Thanks for your reading！I’m a student who is learning population pharmacokinetic modeling using Phoenix NLME. In my Pop CWRES-IVAR plot and Pop CWRES-TAD plot, there is always no blue and red lines regadle… --- ## [Log-transformed plasma concentration-time profiles](https://forum.certara.com/t/log-transformed-plasma-concentration-time-profiles/3734)
**Author:** [@davidq8](https://forum.certara.com/u/davidq8)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 8:41pm UTC](https://forum.certara.com/t/log-transformed-plasma-concentration-time-profiles/3734 "2024-02-06T20:41:14Z")
Hello, I am working on a model, and I need to test the model with plasma concentration to be log-transformed. Is there an option in the software to transform drug exposure data from normal scale to log scale, or should … --- ## [self-define model structure with if, else](https://forum.certara.com/t/self-define-model-structure-with-if-else/3729)
**Author:** [@linda](https://forum.certara.com/u/linda)\ **Replies:** 8\ **Last updated:** [January 19, 2024, 7:02pm UTC](https://forum.certara.com/t/self-define-model-structure-with-if-else/3729 "2024-01-19T19:02:31Z")
Hi Everyone, I am trying to code a self-define model structure with ifelse statements in Phoenix nlme for a pop Pk model. I would like to have a statement like this: t\_0=10 Ac\_0=y0 if t \< Tin ddt\_Ac = k \* Ac - kel … --- ## [calculating inter-individual variability](https://forum.certara.com/t/calculating-inter-individual-variability/2602)
**Author:** [@lwollenberg](https://forum.certara.com/u/lwollenberg)\ **Replies:** 3\ **Last updated:** [December 12, 2023, 10:21pm UTC](https://forum.certara.com/t/calculating-inter-individual-variability/2602 "2023-12-12T22:21:02Z")
Hi, My colleagues and I were having a discussion on calculations regarding the omega and omegastderr output and getting this into useful terms that can help you better understand the variability for the purposes of repor… --- ## [Closed form vs differential equation](https://forum.certara.com/t/closed-form-vs-differential-equation/3720)
**Author:** [@cmukashyaka](https://forum.certara.com/u/cmukashyaka)\ **Replies:** 2\ **Last updated:** [December 12, 2023, 8:50pm UTC](https://forum.certara.com/t/closed-form-vs-differential-equation/3720 "2023-12-12T20:50:02Z")
Hello, I am running a 2-compartment linear model, when I don’t click closed form to use differential equations, the model is not converging with error message: Initial parameter values result in -LL = NaN Restart from… [Next page](https://forum.certara.com/c/phoenix/certara-forums/modelling-and-simulation/27.md?page=1)