Open elgabbas opened 6 months ago
Hi Ahmed,
I'm also interested in this question because of the amount of time it takes to make spatial predictions. I was under the impression that predictEtaMean = TRUE
would speed up prediction as well, so I was also surprised when it slowed it down instead. Have you learned anything since posting this?
Thanks, Clara
Hello Clara,
I am interested in fitting large-scale models using GPP but have also fitted smaller-scale models for exploration.
In relatively small-scale models, using predictEtaMean = TRUE
increased the prediction speed in my case by 3 times.
However, this did not help much when using large-scale models when I predict to new sites [see
here]. When predictEtaMean = TRUE
, the predictlatentfactor function calculates the distances between all sampling units and between sampling units and new sites and do further analyses on them. These two matrices can be very large in large-scale studies and this is probably the reason for the problem in my case. Using predictEtaMean = FALSE
did not help in my case.
Ahmed
Hello,
I would like to make spatial predictions for an Hmsc model with a spatial random effect. I have two questions here:
predict
function is very slow. In a toy model with only c.a. 5000 sampling sites and 22 species, thepredict
function took 25 minutes to run. The final model will be more complex: c.a. 50K sampling sites and many more species.I tried using
nParallel = nChains
argument but this did not improve much the processing speed. I tried to increase the speed by making small changes to thepredict.Hmsc
andpredictLatentFactor
functions to process both functions in parallel. There is some speed improvement, but ifpredictEtaMean = TRUE
orpredictEtaMeanField = TRUE
, no improvement was found.Is it possible to increase the speed of model predictions?
Could you please explain, in less technical terms, what is the difference between the values of the previous three predictions and which should be used? Is there an ecological difference in their interpretation? Using
predictEtaMean = TRUE
orpredictEtaMeanField = TRUE
makes the prediction take much time.Thanks, Ahmed