Hi Jim It is defined and initialised: line 69 in the differential equation: dmCaT_soma_AB <- (mCaTx(v_soma) - mCaT_soma_AB)/taumCaT(v_soma) and initialised in line 83 dmCaT_soma_AB=0
However, l just noticed the mistake. It needs to be initialised without the d, i.e. mCaT_soma_AB=0 and not dmCaT_soma_AB Regards Jannetta Regards Jannetta On 2 June 2013 02:14, jim holtman <[email protected]> wrote: > 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 <[email protected]>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]] >> >> ______________________________________________ >> [email protected] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> 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. > -- =================================== Web site: http://www.jannetta.com Email: [email protected] =================================== [[alternative HTML version deleted]] ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
