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I have a system of ode including 3 diff equation. I found two parameters Tcell and CD19 by experiment over time. Here is my dataset:

data1 = {{1, 1, 6734}, {1, 1.5, 8734}, {1, 2, 12826}, {1, 2.5, 
20826}, {1, 3, 34006}, {1, 3.5, 30006}, {1, 4, 26975.5}, {1, 4.5, 
20975.5}, {1, 5, 15307}, {1, 5.5, 13307}, {1, 6, 12307}, {2, 1, 
9222.5}, {2, 1.5, 9222.5}, {2, 2, 8653}, {2, 2.5, 7523}, {2, 3, 
6002}, {2, 3.5, 5002}, {2, 4, 3996}, {2, 4.5, 3002}, {2, 5, 
1985}, {2, 6, 1237}};

now I have some known rate parameters such as kpCD19 & kaCD19 and by parametricNDSolveValue, I am trying to find unknown parameters such as kD, kkill, kdecayT, koff, kon. I also have a set of differential equations that I want to fit data to these equatsions

kpCD19 = 0.5; kaCD19 = 0.2;tmax = 6;
ode = {Tcell'[t] == -kon * Tcell[t] *CD19[t] + koff * complex[t] + 
 kD* Tcell[t] -  kdecayT Tcell[t], CD19'[t] == 
kpCD19* CD19[t] - kaCD19* CD19[t] - kon * Tcell[t] *CD19 [t] + 
 koff *complex[t] - kkill*CD19[t], complex'[t] == 
kon *Tcell[t]*CD19[t] - koff *complex[t] - kD* Tcell[t], Tcell[0] == 5000, CD19[0] == 10000, complex[0] == 0};

paramSOL = ParametricNDSolveValue[ode, {Tcell, CD19, complex}{t, 0, tmax}, {kD, kkill, kdecayT,nkoff, kon}, WorkingPrecision ->100]



model[kD_, kkill_, kdecayT_, koff_, kon_][i_, t_] := 
Through[paramSOL[kD, kkill, kdecayT, koff, kon][t], List][[i]] /; And @@ NumericQ /@ {kD, kkill, kdecayT, koff, kon, i, t}    

then I fit my model by NonlinearModelfit but it seems that it did not fit it good since the Rsquared is 0.09

fitted = NonlinearModelFit[data1, model[kD, kkill, kdecayT, koff, kon][i, t], {{kD, 0.1}, {kkill, 0.1}, {kdecayT, 0.1}, {koff,   0.1}, , {kon, 0.1}}, {i, t}, WorkingPrecision -> 100] // Quiet;

fitted["RSquared"]]
fitted["ParameterTable"]
fitted["ParameterErrors"][[2]]

dataTcell = Take[data1, 12][[All, 2 ;; 3]]
dataBcell = Drop[data1, 12][[All, 2 ;; 3]]
Show[ListPlot[{dataTcell, dataBcell}, PlotLegends -> {"Tcell"},Frame -> True], Plot[{fitted[1, t], fitted[2, t]}, {t, 0, tmax}]]

when I graph the fit also it seems that it could not fit the data correctly. My question is what is the problem that it could not fit data correctly?

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    $\begingroup$ First of all, please do not just post a large block of code without any comments on what is what. Secondly, there are a lot of variables and functions in that code that are not defined here. It is not possible to help you if you do not provide all the data. Please try to find a minimal example showing what goes wrong, post it in its entirety here such that we can just copy paste it into our own notebooks and run it. $\endgroup$
    – a20
    Aug 26 at 11:26
  • $\begingroup$ You might be better off using NMinimize. For example, see "Model calibration with phase space data" or "Fitting for constants". $\endgroup$ Sep 18 at 19:18
  • $\begingroup$ Thanks Anton, but I could not figure out how to fit my differential equation to the model.Nminimize is just fitting data. $\endgroup$
    – Farnaz
    Sep 22 at 22:32

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