I just did a search through the source and never did find a place that
'mCaT_soma_AB' was defined. How can you expect to use it if it has not
been defined.
On Sat, Jun 1, 2013 at 8:50 PM, Jannetta Steyn <janne...@henning.org> wrote:
> Hi All
>
> I am trying to implement a neural model in R from a paper but I have run
> into a bit of a problem. The model is getting so complex that I can't
> really test it in bits any more. At the moment I get this error:
> Error in eval(expr, envir, enclos) : object 'mCaT_soma_AB' not found
>
> I think I have been staring at it too long because I can't see what I have
> done wrong. Can anyone perhaps spot the error I have made. The full code is
> posted below.
>
> Many thanks
> Jannetta
>
> # TODO: Add comment
> #
> # Author: a9912577
>
> ###############################################################################
>
>
> library(deSolve)
>
> ST <- function(time, init, parms) {
> with(as.list(c(init, parms)),{
> #functions to calculate activation m and inactivation h of the currents
> mNax <- function(v) 1/(1+exp(-(v+24.7)/5.29));
> taumNa <- function(v) 1.32 - (1.26/(1+exp(-v+120)/25));
> hNax <- function(v) 1/(1+exp((v+48.9)/5.18));
> tauhNa <- function(v) (0.67/(1+exp(-(v+62.9)/10))) *
> (1.5+1/(1+exp(v+34.9)/3.6));
> mCaTx <- function(v) 1/(1+exp(-(v+25)/7.2))
> taumCaT <- function(v) 55-(49.5/(1+exp(-(v+58)/17)))
> hCaTx <- function(v) 1/(1+exp((v+36)/7))
> tauhCaT_AB <-function(v) 87.5-(75/(1+exp(-(v+50)/16.9)))
> tauhCaT_PD <-function(v) 350-(76/(1+exp(-(v+50)/16.9)))
> mCaSx <- function(v) 1/(1+exp(-(v+22)/8.5))
> taumCaS <- function(v) 16-(13.1/(1+exp(-(v+25.1)/26.5)))
> mNapx <- function(v) 1 / (1+exp(-(v+26.8)/8.2))
> taumNap <- function(v) 19.8-(10.7/(1+exp(-(v+26.5)/86.)))
> hNapx <- function(v) 1/1+exp((v+48.5)/4.8)
> tauhNap <- function(v) 666-(379/(1+exp(-(v+33.6)/11.7)))
> mhx <-function(v) 1/(1+exp((v+70)/6))
> taumh <- function(v) 272+(1499/(1+exp(-(v+42.2)/8.73)))
> mKx <- function(v) 1/(1+exp(-(v+14.2)/11.8));
> taumK <- function(v) 7.2-(6.4/(1+exp(-(v+28.3)/19.2)))
> # AB soma
> iCaT_soma_AB <- gCaT_soma_AB * mCaT_soma_AB ^ 3 * hCaT_soma_AB * (v_soma -
> ECaT_soma_AB)
> iCaS_soma_AB <- gCaS_soma_AB * mCaS_soma_AB ^ 3 * (v_soma - ECaS_soma_AB)
> iNap_soma_AB <- gNap_soma_AB * mNap_soma_AB ^ 3 * hNap_soma_AB * (v_soma -
> ENap_soma_AB)
> ih_soma_AB <- gh_soma_AB * mh_soma_AB ^ 3 * hh_soma_AB * (v_soma -
> Eh_soma_AB)
> iK_soma_AB <- gK_soma_AB * mK_soma_AB ^ 4 * mK_soma_AB * (v_soma -
> EK_soma_AB)
> iKCa_soma_AB <- gKCa_soma_AB * mKCa_soma_AB ^ 4 * (v_soma - EKCa_soma_AB)
> # Total current for Calcium
> totalICa <- iCaT_soma_AB + iCaS_soma_AB
> # Differential equations
> dCaConc_soma <- (-F_AB * totalICa - CaConc_soma + C0_AB)/tauCa_AB
> mKCax_AB <- function(v, CaConc_soma)
> (CaConc_soma/(CaConc_soma+30))*(1/(1+exp(-(v+51)/4)))
> mKCax_PD <- function(v, CaConc_soma)
> (CaConc_soma/(CaConc_soma+30))*(1/(1+epx(-(v+51)/8)))
> taumKCa <-function(v) 90.3 - (75.09 / (1+exp(-(v+46)/22.7)))
> mAx <- function(v) 1/(1+exp(-(v+27)/8.7))
> taumA <- function(v) 11.6-(10.4/(1+exp(-(v+32.9)/15.2)))
> hAx <- function(v) 1 / (1+exp((v+46.9)/4.9))
> tauhA <- function(v) 38.6 - (29.2/(1+exp(-(v+38.9)/26.5)))
> mProcx <- function(v) 1 / (1+exp(-(v+12)/3.05))
> taumProc <- 0.5
> # Currents as product of maximal conducatance(g), activation(m) and
> inactivation(h)
> # Driving force (v-E) where E is the reversal potential of the particular
> ion
> # AB axon
> iNa_axon_AB <- gNa_axon_AB * mNa_axon ^ 3 * hNa_axon * (v - ENa_axon_AB)
> iK_axon_AB <- gK_axon_AB * mK_axon ^ 4 * (v - EK_axon_AB)
> iLeak_axon_AB <- gLeak_axon_AB * (v - ELeak_axon_AB)
> dv <- (0 - iNa_axon_AB - iK_axon_AB - iLeak_axon_AB) / C_axon_AB
> dmNa_axon_AB <- (mNax(v) - mNa_axon_AB)/taumNa(v)
> dhNa_axon_AB <- (hNax(v) - hNa_axon_AB)/tauhNa(v)
> dmK_axon_AB <- (mKx(v) - mK_axon_AB)/taumK(v)
> dv_soma <- (I - iCaT_soma_AB - iCaS_soma_AB - iNap_soma_AB - ih_soma_AB -
> iK_soma_AB - iKCa_soma_AB)
> dmCaT_soma_AB <- (mCaTx(v_soma) - mCaT_soma_AB)/taumCaT(v_soma)
> dhCaT_soma_AB <- (hCaTx(v_soma) - hCaT_soma_AB)/tauhCaT_AB(v_soma)
> dmCaS_soma_AB <- (mCaSx(v_soma) - mCaS_soma_AB)/taumCaS(v_soma)
> dmNap_soma_AB <- (mNapx(v_soma) - mNap_soma_AB)/taumNap(v_soma)
> dhNap_soma_AB <- (hNapx(v_soma) - hNap_soma_AB)/tauhNap(v_soma)
> dmh_soma_AB <- (mhx(v_soma) - mh_soma_AB)/taumh(v_soma)
> dmK_soma_AB <- (mKx(v_soma) - mK_soma_AB)/taumK(v_soma)
> dmKCa_soma_AB <- (mKCax_AB(v_soma,CaConc_soma) -
> mKCa_soma_AB)/taumKCa(v_soma)
> list(c(dv,dv_soma,dmNa_axon_AB, dhNa_axon_AB, dmK_axon_AB, dmCaT_soma_AB,
> dhCaT_soma_AB, dmCaS_soma_AB, dmNap_soma_AB, dhNap_soma_AB, dmh_soma_AB,
> dmK_soma_AB, dmKCa_soma_AB,dCaConc_soma))
> })}
> ## Set initial state
> init = c(dv=-55,dv_soma=-55,dmNa_axon_AB=0, dhNa_axon_AB=0, dmK_axon_AB=0,
> dmCaT_soma_AB=0, dhCaT_soma_AB=0, dmCaS_soma_AB=0, dmNap_soma_AB=0,
> dhNap_soma_AB=0, dmh_soma_AB=0, dmK_soma_AB=0,
> dmKCa_soma_AB=0,dCaConc_soma=0)
> ## Set parameters
> F_AB=0.418
> C0_AB=0.5
> tauCa_AB=303
>
> ENa_axon_AB=50
> EK_axon_AB=-80
> ELeak_axon_AB=-60
>
> gNa_axon_AB=0.300
> gK_axon_AB=0.0525
> gLeak_axon_AB=20
>
> C_axon_AB=0.0015
>
> ECaT_soma_AB=55.2e-3
> ECaS_soma_AB=9e-3
> ENap_soma_AB=50
> Eh_soma_AB=-20
> EK_soma_AB=-80
> EKCa_soma_AB=-80
> EA_soma_AB=-8
> EP_soma_AB=0
> ELeak_soma_AB=-50
>
> gCaT_soma_AB=55.2e-3
> gCaS_soma_AB=9e-3
> gNap_soma_AB=2.7e-3
> gh_soma_AB=0.00054
> gK_soma_AB=0.0525
> gKCa_soma_AB=0.600
> gA_soma_AB=0.0216
> gP_soma_AB=0.570
> gLeak_soma_AB=0.000045
> gAxial_soma_AB=0.003
> gGap_AB=0.75e-3
> C_soma_AB=9e-3
>
> F_PD=0.515
> C0_PD=0.5
> tauCa_PD=300
>
> I=6.5
> parms =
>
> c(ENa_axon_AB,EK_axon_AB,ELeak_axon_AB,gNa_axon_AB,gK_axon_AB,gLeak_axon_AB,C_axon_AB,ECaT_soma_AB,ENap_soma_AB,Eh_soma_AB,EK_soma_AB,EKCa_soma_AB,EA_soma_AB,EP_soma_AB,ELeak_soma_AB,gCaT_soma_AB,gCaS_soma_AB,gNap_soma_AB,gh_soma_AB,gK_soma_AB,gKCa_soma_AB,gA_soma_AB,gP_soma_AB,gLeak_soma_AB,gAxial_soma_AB,C0_AB,C0_PD)
> ## Set integrations times
> times = seq(from=0, to=100, by = 0.25);
>
> out<-ode(y=init, times=times, func=ST, parms=parms)
> plot(out)
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
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