[R] help mkin

[rebekka baumgartner]

Sorry, I copied in the wrong error message, this is the right one:
Model cost at call  1 :  15535.3 
DLSODA-  Warning..Internal T (=R1) and H (=R2) are                              
      such that in the machine, T + H = T on the next step                      
     (H = step size). Solver will continue anyway.                              
      In above,  R1 =  0.0000000000000D+00   R2 =  0.0000000000000D+00          
DINTDY-  T (=R1) illegal                                                        
      In above message,  R1 =  0.1500000000000D+02                              
      T not in interval TCUR - HU (= R1) to TCUR (=R2)                          
      In above,  R1 =  0.0000000000000D+00   R2 =  0.0000000000000D+00          
DINTDY-  T (=R1) illegal                                                        
      In above message,  R1 =  0.2900000000000D+02                              
      T not in interval TCUR - HU (= R1) to TCUR (=R2)                          
      In above,  R1 =  0.0000000000000D+00   R2 =  0.0000000000000D+00          
DLSODA-  Trouble in DINTDY.  ITASK = I1, TOUT = R1                              
      In above message,  I1 =         1                                         
      In above message,  R1 =  0.2900000000000D+02                              
Error in lsoda(y, times, func, parms, ...) : 
  illegal input detected before taking any integration steps - see written message

-------- Original-Nachricht --------
> Datum: Tue, 02 Nov 2010 11:44:32 +0100
> Von: "rebekka baumgartner" <rebekka.b at gmx.ch>
> An: r-help at r-project.org
> Betreff: [R] help mkin

> 
> Hi,
> I am trying fit my kinetic data with the "mkin" package. There I have two
> questions:
> 
> 1.) I would like to fix the parameter parent_0, the concentration of the
> parent at time 0. In the mkinfit function description it says you can do it
> with the arguments parms.ini and fixed_parms. In which form do these
> arguments have to be to fix the (internally defined and fitted) parameter
> parent_0?
> SFO <- mkinmod(parent=list(type="SFO"))
> SFO.fit <- mkinfit(SFO,data, parm.ini=??, fixed_parms=??)
> 
> 2.) When I try to fit the parent and a metabolite m1, I get the error
> message:
> Error in dnorm(x, mean, sd, log) : 
>   Non-numeric argument to mathematical function
> In addition: Warning messages:
> 1: In Ops.factor(ModVar, obsdat) : - not meaningful for factors
> 2: In Ops.factor(ModVar, obsdat) : - not meaningful for factors
> 
> My code is:
> data <- read.table("101025_batch1.txt", header=TRUE)
> SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1", sink =TRUE),m1 =
> list(type = "SFO")) 
> SFO.fit <- mkinfit(SFO_SFO,data)
> 
> 101025_batch1.txt looks like this:
> name	time	value
> parent	0	NA
> parent	15	NA
> parent	29	23.796
> parent	44	14.499
> parent	58	7.650
> parent	73	4.170
> parent	88	2.438
> parent	102	1.865
> parent	117	1.598
> m1	0	0
> m1	15	6.476
> m1	29	19.651
> m1	44	32.271
> m1	58	40.906
> m1	73	48.295
> m1	88	53.295
> m1	102	56.250
> m1	117	58.459
> 
> Thank you very much for you help!
> Rebekka
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