similar to: Getting 'LinkingTo' to find the right library

In the following code routine 'initaquaphy' is defined in Fortran, and dynamically loaded into R.: test.f: subroutine initaquaphy(odeparms) external odeparms double precision pars(19) common /myparms/pars call odeparms(19, pars) return end $ R CMD SHLIB Aquaphy.f gfortran -fpic -g -O2 -c test.f -o test.o gcc -std=gnu99 -shared

I have a problem integrating the 'standard map' ( http://en.wikipedia.org/wiki/Standard_map http://en.wikipedia.org/wiki/Standard_map ) with deSolve: By using the modulo-operator '%%' with 2*pi in the ODEs (standardmap1), the resulting values of P and Theta, should not be greater than 2pi. Because this was not the case, i was thinking that the function 'ode' has some

Hi folks, I am having a small problem with asterisk-1.6.2.7 + app_fax on OpenBSD 4.7 -release. Everything seems to work fine. I have a macro which answers, receives the fax to a tiff, and then runs a script (mailfax) to convert that to pdf and email it. It all works perfectly except for some errors I am seeing in the console. After it hangs up I get a dozen or so messages in the cli

I was flummoxed for a long time by errors generated when I did something like install.packages(foo,lib="Rlib") where ``Rlib'' is my personalized directory of R packages, which lives in my home directory (from which I started R before issuing the foregoing install.packages() call. Recently someone (I forget who, but thanks very much to whomever it was) pointed out that I

Hello, I am solving a set of ODEs using deSolve and have run into a problem I would appreciate some advice on. One of the parameters (m) in the ODEs changes between two states when one of the variables (D) crosses a threshold (D_T) for the first time in either direction. Additionally, when the variable crosses the threshold (either by increasing or decreasing), there is a time delay (delay)

> On Apr 18, 2018, at 1:04 AM, Hannah Meredith <hrmeredith12 at gmail.com> wrote: > > Hello, > > I am solving a set of ODEs using deSolve and have run into a problem I > would appreciate some advice on. One of the parameters (m) in the ODEs > changes between two states when one of the variables (D) crosses a > threshold (D_T) for the first time in either direction.

Hi there R-helpers: I'm having problems with the function ode() found in the package deSolve. It seems that when my state variables are too numerous (>33000 elements), the function throws the following error: Error in vode(y, times, func, parms, ...) : cannot allocate memory block of size 137438953456.0 Gb In addition: Warning message: In vode(y, times, func, parms, ...) : NAs

On Mon, 30 Apr 2007 bill at insightful.com wrote: > On Tue, 10 Apr 2007 timh at insightful.com wrote: > > > I've created a .Rd file (below), then converted that to .sgml using > > R CMD Rdconv --type=Ssgm combn.Rd > combn.sgml > > The output (shown below) is missing some of the sections: > > arguments > > seealso > > examples > > If

Hi All Having been pointed the use of events and roots in deSolve, I was able to implement the Izchikevich model of spiking neurons. However, I'm not too sure of defining the event. The deSolve documentation says: An event is triggered when the ball hits the ground (height = 0) Then velocity (y2) is reversed and reduced by 10 percent. The root function, y[1] = 0, triggers the event: >

Hi, I have used DeSolve package for my ODE problem regarding infectious disease transmission and currently am trying to pass lots (roughly a thousand) of model parameters to the C compiled model (I have to use C compiled code instead of R code purely because of the speed). I can't go define it one by one as it gonna take ages to finish and also quite difficult to revise. I have read the

Hi, I've solved a simple differential equation describing the degradation of amino acid carbon (THAA-C) using deSolve. Code is a follows: # Input of model parameters, a and b describes form of curve, i is apparent initial age of Org. C. parameters <- c(a = a, b = b, i=i) # Initial value of the model, G state = c(G = G) #specifies the function degradation as a function of

Hello, I've been trying to make LinkingTo work when the package linked to has c++ code. I've put dumb packages to illustrate this emails here ; http://addictedtor.free.fr/misc/linkingto Package A defines this C++ class: class A { public: A() ; ~A() ; SEXP hello() ; } ; Package B has this function : SEXP say_hello(){ A a ; return a.hello() ; } headers of package A are copied

Dear list The deSolve package allows you to specify the model code in C or Fortran. Thanks to the excellent vignette this works fine. However I have not yet managed to use forcing functions in C code. In pure R code this works very well with approxfun() specified outside the model: ############################################### #Model lvml <- function(t, x, parms) {

I previously sent a cri de coeur about this problem to the r-help list but so far have not managed to extract a solution. So I am trying here. (Uh, Ubuntu *is* a "special instance" of Debian, isn't it?) The problem is that I cannot install rgdal, and I need it. Rather desperately. I do: install.packages("rgdal",lib="/home/rolf/Rlib") and get the error

I am working on a SLES 10 cluster with R available on it. To better use my resources, I want to use Rmpi, but I am having a difficult time installing it. I have set the $R_LIBS variable correctly. The MPI libraries are available through the PGI compiler, but this R instance was compiled with GCC. The Rmpi package can be compiled and installed with %R CMD INSTALL Rmpi_0.5-5.tar.gz

I'm just getting to grips with using ode function and have used the examples and vignettes to produce a small model of a one-pool, michaelis-menten, enzyme kinetic reaction. The rate of flux of substrate into pool A is constant (fluxoa) however the rate of flux out of pool A is controlled by the HMM equation (v = Vmax/ ( 1 + (Km / Concentration A )) ). This function works fine and

I've just installed version 1.4.0 of R, and am experiencing a puzzling phenomenon with the library() function. I have .lib.loc set as follows: > .lib.loc [1] "/usr/local/lib/R/library" "/home/faculty/rolf/Rlib" If I invoke > library(melvin) I get the error message Error in library(melvin) : There is no package called `melvin' but if I invoke >

Hi, Sorry for posting a question that has been asked before but I couldn't quite find the right answer in previous help topics. I am trying to set my library path to a user-specified library ("C:/Users/K/Documents/Work/RLib"). I have used .libPaths("C:/Users/K/Documents/Work/RLib") but when I check the .libPaths(), both the user-specified and default libraries appear. It

Hello, I'm trying to do some differential equation modeling in R using the package 'deSolve.' Briefly, I'm trying to use the law of mass action (the details of which aren't really important) to structure a vector of rate equation which will be passed into an ODE function and solved with associated functions from 'deSolve.' Roughly what this entails is scanning

Hi All It has been suggested to me that the folks in this list might be able to help me out of my misery. As part of my learning curve to building a rather detailed model of a small neurone complex I am implementing some existing models in R. For the moment I want to implement the Izhikevich model as described in his 2003 paper. The equations are as follows: v' = 0.04v^2 + 5v + 140 - u - I