search for: rtol

Dear All, I was wondering whether any one knows of a matrix bending function in R that can turn non-positive definite matrices into the nearest positive definite matrix. I was hoping there would be something akin to John Henshall's flbend program (http://agbu.une.edu.au/~kmeyer/pdmatrix.html), which allows the standard errors of the estimated matrix elements to be considered in the

...odel <- function(time, y, parms) { dCpdt <- -(parms["Vm"]/parms["Vd"])*y[1]/(parms["Km"]+y[1]) list(dCpdt)} Dose<-300 modfun <- function(time,Vm,Km,Vd) { out <- lsoda(Dose/Vd,time,mm.model,parms=c(Vm=Vm,Km=Km,Vd=Vd), rtol=1e-8,atol=1e-8) out[,2] } objfun <- function(par) { out <- modfun(PKindex$time,par[1],par[2],par[3]) sum((PKindex$conc-out)^2) } fit <- optim(c(10,1,80),objfun, method="Nelder-Mead) print(fit$par) [1] 10.0390733 0.1341544 34.9891829 #--Km=0.1341544,wrong value--...

Hello, I wanted to test the odesolve package and tried to use compiled C-code. But when I do: erg <- lsoda(y, times, "mond", parms, rtol, atol, tcrit=NULL, jacfunc=NULL, verbose=FALSE, dllname="mond", hmin=0, hmax=Inf) I get the error message: Error in lsoda(y, times, "mond", parms, rtol, atol, tcrit = NULL, jacfunc = NULL, : Unable to find mond in mond The C co...

...s needed for that system of equations. Why is it needed? For my function below ('lvcomp2'), I don't know what global values lsoda needs at each point in time (see???), other than the previous time step's values of y and the parms. Any help? Also, any rule of thumb advice regarding rtol and atol would be appreciated. p <- c(r1=.01, r2=.01, a12=0.5, a21=0.6, k1=1,k2=1) t <- 1:20 lvcomp2 <- function(y, t, p) { # Lotka - Volterra model of two competing populations dN1.dt <- p["r1"] * y[1] * (1-(y[1] + p["a12"]*y[2])/p["k1"]) dN2.dt <- p[&...

...ms) and the results look not unreasonable: out<-as.data.frame(out) par(mfrow=c(4,1)) for (i in 2:(dim(out)[2]))plot(out[,1],out[,i], pch=".", xlab="time", ylab=names(out)[i]) If I try doing the same thing with lsoda: out <- lsoda(y=y,times=times,func=func, parms=parms, rtol=1e-1, atol= 1e-1) I run into problems with a series of 'Excessive precision requested' warnings with no output beyond the first time point. Fiddling with rtol and atol doesn't seem to do very much. What is likely to be causing this (I'm guessing the wide range of the absolute val...

I'm solving the differential equation dy/dx = xy-1 with y(0) = sqrt(pi/2). This can be used in computing the tail of the normal distribution. (The actual solution is y(x) = exp(x^2/2) * Integral_x_inf {exp(-t^2/2) dt} = Integral_0_inf {exp (-xt - t^2/2) dt}. For large x, y ~ 1/x, starting around x~2.) I'm testing both lsoda and rk4 from the package odesolve. rk4 is accurate using step

...require(odesolve) parms <- c(k1 = 0.04, k2 = 1e4, k3=3e7) my.atol <- c(1e-6, 1e-10, 1e-6) times <- c(0, 4*10^(-1:10)) print(system.time( out1 <- lsoda(c(1.0,0.0,0.0),times,"myderivs", parms, rtol=1e-4,atol=my.atol,jacfunc="myjac", dllname="mymod") ) ) ### END When I run this mymod.c compiles without any errors or warnings and the mymod.so library seems to load fine via dyn.load (the call is.loaded("mymod&...

..., dAve, dAlu, dAli, dAbr, dAh, dApa, dAsp, dAgi, dAk, dAm, dAad, dAsk), Car = Car, Cve=Cve, Clu=Clu, Cli=Cli, Cbr=Cbr, Ch=Ch, Cpa=Cpa, Csp=Csp, Cgi=Cgi, Ck=Ck, Cm=Cm, Cad=Cad, Csk=Csk)) }) } ODE <- as.data.frame(daspk(y = y, times = times, func = Fun_ODE, parms = pars, atol = 1e-10, rtol = 1e-10)) -- Dr In-Sun Nam Knutsson Research Associate The Centre for Applied Pharmacokinetic Research (CAPKR) School of Pharmacy and Pharmaceutical Sciences University of Manchester Stopford Building Oxford Road Manchester U.K. Phone: +44 161 275 2355 Email: In-sunnam.Knutsson@manchester.ac.u...

...e time cleaning up the description so a commit may look like: > > ``` > RFC: treat small negative λ as 0 for sqrt(::Hermitian) (#35057) > > * treat small negative λ as 0 for sqrt(::Hermitian) and log(::Hermitian) > > * typo > > * added tests, docs; removed rtol argument for log > > * don't ask for rtol so close to eps(Float64) > ``` There are some inelegant ways to workaround that problem (see, for example, https://github.com/material-foundation/github-squash-and-merge-pr-descriptions if you are using Chrome). I think I suggested GitHub...

...c=c(32,28,25,22,18,14,11)) Dose<-200 Tinf <-0.5   defun<- function(time, y, parms) {  dCpdt <- -parms["kel"] * y[1]  list(dCpdt)  } modfun <- function(time,kel, Vd) {   out <- lsoda(((Dose/Tinf)*(1/(kel*Vd)))*(1-exp(-kel*time)),c(0,time),defun,parms=c(kel=kel,Vd=Vd),rtol=1e-3,atol=1e-5)  out[-1,2]  } objfun <- function(par) {  out <- modfun(PKindex$time, par[1], par[2])  gift <- which( PKindex$conc != 0 )  sum((PKindex$conc[gift]-out[gift])^2)  }        gen<-genoud(objfun,nvars=2,max=FALSE,pop.size=30,max.generations=100,wait.generations=100,starting....

...f (t < tin) R <- (D/tin) else R <- 0   dy1 <- R - (p["k12"]+p["k"])* y[1] + p["k21"]*y[2]   dy2 <- p["k12"]* y[1] - p["k21"] *y[2]   list(c(dy1, dy2)) }   p <- c(k=k, k12=k12, k21=k21, V=V) result <- lsoda( yini, times, pkmod, p,rtol = 1e-08, atol = 1e-08,events = list(data = events)) result <- data.frame(result) names(result) <- c("time","Amount1", "Amount2") plot(result$Amount1 ~ result$time, type="b", main="Central", xlab="time", ylab="Amount") plot(...

...deas / comments about why I am receiving the following warning when I run lsoda: 1: lsoda-- at t (=r1), too much accuracy requested in: lsoda(start, times, model, parms) 2: for precision of machine.. see tolsf (=r2) in: lsoda(start, times, model, parms) I have tried changing both rtol and atol but without success. I saw the thread in the R-archive of 11 June 2004 but this has not helped me. I have built the model in stages and the problem only occurs when the exponent beta in the third DE is anything other than 0 or 1. If beta = 0 or 1 then the solver gives me perfectly ju...

...ot;] * y[1] + p["k2"] * y[2]*y[3] > if(y[3] < .4) yd3 <- -y[3] ### These if,else statements are new > else yd3 <- p["k3"] * y[2]^2 > list(c(yd1,-yd1-yd3,yd3),c(massbalance=sum(y))) > } > out <- lsoda(c(.5,0,.5),times,lsexamp, parms, rtol=1e-4, atol= my.atol, > hmax=.1) > matplot(out[,1],out[,2:5], type="l") > out[dim(out)[1],] # The intent of my could was to cause population 1 to > fall to zero as soon as it reached < 0.4. However, the populations 1 > and 2 reach approximations of 0 (4e-281 and 5e-11)....

...quivalent operation at the same precision level. It is very easy for codes to be very slightly different and give quite widely different output. Indeed, even without the trace, we see (zeroin from rootoned here) > zeroin(ff, c(0, 10), trace=FALSE) $root [1] 1.386294 $froot [1] -5.658169e-10 $rtol [1] 7.450581e-09 $maxit [1] 9 > uniroot(ff, c(0, 10), trace=FALSE) $root [1] 1.38629 $f.root [1] -4.66072e-06 $iter [1] 10 $init.it [1] NA $estim.prec [1] 6.103516e-05 > Is the lack of trace a bug, or at least an oversight? Being able to follow iterations is a classic approach to chec...

...-- t (=r1) illegal Warning: t not in interval tcur - hu (= r1) to tcur (=r2) Warning: intdy-- t (=r1) illegal Warning: t not in interval tcur - hu (= r1) to tcur (=r2) Warning: lsoda-- trouble from intdy. itask = i1, tout = r1 Error in lsoda(y = y0, times = times, fderiv, parms = c(mod = mod), rtol = 1e-04, : Illegal input to lsoda R version: 2.3.0 (2006-04-24) >gcc --version gcc (GCC) 3.4.2 (mingw-special) Copyright (C) 2004 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR...

A couple of minor points about the odesolve package (which I am otherwise enjoying very much): 1. "scalar" is misspelled as "scaler" in the definitions of the rtol and atol parameters 2. it is possible to crash R by doing something dumb, e.g failing to read the documentation carefully enough and (a) returning only a vector of derivatives and not a list of (derivatives, global values) and (b) making the derivative vector shorter than the vector of initial co...

On Fri, Sep 11, 2020 at 6:53 PM David Blaikie <dblaikie at gmail.com> wrote: > Is there any observable difference between "Squash and Merge" or "Rebase > and Merge" when "enforce linear history" is enabled, then? > "Squash and Merge" will only generate one commit. > > On Fri, Sep 11, 2020 at 3:45 PM Stephen Neuendorffer via llvm-dev

...ot;k") { I=x[1] dI=-w["mu"]*I+w["beta0"]*exp(-w["k"]*t)*(1-I) list(c(dI),c(S=1-I)) } output = lsoda(c(I_mod),times,ODE_sys, parms, rtol=1e-6, atol= my.atol) return(output) } # The negative log likelihood of this model given a data set "new". This works fine if it is used in the optim() routine with only one data set. NLL=function(coef) { beta0=coef[1] mu=coef[2] k=coef[3]...

...ly > different and give quite widely different output. > > Indeed, even without the trace, we see (zeroin from rootoned here) > > > zeroin(ff, c(0, 10), trace=FALSE) > $root > [1] 1.386294 > > $froot > [1] -5.658169e-10 > > $rtol > [1] 7.450581e-09 > > $maxit > [1] 9 > > > uniroot(ff, c(0, 10), trace=FALSE) > $root > [1] 1.38629 > > $f.root > [1] -4.66072e-06 > > $iter > [1] 10 > > $init.it <http://init.it> > [1]...

...0.02, k2=250, E=0.01); pars yini <- c(S=0.01, ES = 0.01, P=0.0, E=0.01); yini times <- seq(0, 0.01, by = 0.0001); times dyini = c(dS=0.0, dES=0.0, dP=0.0) ## Tabular output check of matrix output DAE <- daspk(y = yini, dy = dyini, times = times, res = Res_DAE, parms = pars, atol = 1e-10, rtol = 1e-10) ERROR: daspk-- warning.. At T(=R1) and stepsize H (=R2) the nonlinear solver f nonlinear solver failed to converge repeatedly of with abs (H) = H repeatedly of with abs (H) = HMIN preconditioner had repeated failur 0.0000000000000D+00 0.5960464477539D-...