Re: [R] deSolve package

2015-10-17 Thread Thomas Petzoldt
Dear Andre, some people would be happy to assist you, but your code fragment is incomplete, so diagnosing your problem was impossible. Please read the posting guide and provide a minimum reproducible example. Furthermore I wonder why you use dede and not ode, and why sum() with empty parenth

Re: [R] No speed up using the parallel package and ncpus > 1 with boot() on linux machines

2015-10-17 Thread Jeff Newmiller
None of this is surprising. If the calculations you divide your work up into are small, then the overhead of communicating between parallel processes will be a relatively large penalty to pay. You have to break your problem up into larger chunks and depend on vector processing within processes

Re: [R] No speed up using the parallel package and ncpus > 1 with boot() on linux machines

2015-10-17 Thread Milan Bouchet-Valat
Le samedi 17 octobre 2015 à 17:18 +0100, Chris Evans a écrit : > I think I am failing to understand how boot() uses the parallel > package on linux machines, using R 3.2.2 on three different machines > with 2, 4 and 8 cores all results in a slow down if I use "multicore" > and "ncpus". Here's the

[R] No speed up using the parallel package and ncpus > 1 with boot() on linux machines

2015-10-17 Thread Chris Evans
I think I am failing to understand how boot() uses the parallel package on linux machines, using R 3.2.2 on three different machines with 2, 4 and 8 cores all results in a slow down if I use "multicore" and "ncpus". Here's the code that creates a very simple reproducible example: bootReps <- 5

[R] igraph -- Selecting closest neighbors

2015-10-17 Thread Michael Haenlein
Dear all, I am looking for a function to select the N closest neighbors (in terms of distance) of a vertex in igraph. Assume for example N=7. If the vertex has 3 direct neighbors, I would like that the function selects those 3 plus a random 4 among the second degree neighbors. Is there some way

Re: [R] optimization problem

2015-10-17 Thread Berend Hasselman
Your model is producing -Inf entries in the vector Be (in function modl and LL) at some stage during the optimization process. You should first do something about that before anything else. Berend > On 17 Oct 2015, at 03:01, Bert Gunter wrote: > > I made no attempt to examine your details fo