blackrim
how to choose the best smoothing from treePL
Hi, I also attached my questions here, hope the answers would be helpful for other people, or some other people can help as well.
I'm using treePL to do the dating. and I acknowledged that the smoothing parameter is very important, which affects the penalty for rate variation over the tree.
So before I do the dating, I have conducted cross-validation procedure (thorough, prime, randomcv) to determine the best smoothing parameter with different "smooth =" settings (e.g.,smooth = 0.1,1,10,100,1000,10000) in the cross-validation configure file.
now I'm confused facing these “priming” results, which should I choose? or none of them are best?
When "smooth = 0.1", the result is "best: 1(1) bestad: 1 (1) bestcv: 3 (0)", is this best? what does "0" in "bestcv: 3 (0)" mean?
Thank you very much!
Miao
Parts of results are attached below:
==> treePL2769972_0.1.out <== you may want to set the plsimaniter > 100000 result: 4 final: 3128607.6 diff: 355884.83 best: 1(1) bestad: 1 (1) bestcv: 3 (0) PLACE THE LINES BELOW IN THE CONFIGURATION FILE opt = 1 moredetail optad = 1 moredetailad optcvad = 3
==> treePL2769972_1.out <== final: 3207121.5 diff: 110930.04 setting NLOPT parallel : LD_MMA you may want to set the plsimaniter > 100000 result: 4 final: 3000710.2 diff: 317341.38 best: 1(0) bestad: 1 (0) bestcv: 3 (0) PLACE THE LINES BELOW IN THE CONFIGURATION FILE opt = 1 optad = 1 optcvad = 3
==> treePL2769972_10.out <== you may want to set the plsimaniter > 100000 result: 4 final: 3050738.9 diff: 2588895 best: 1(1) bestad: 1 (1) bestcv: 0 (0) PLACE THE LINES BELOW IN THE CONFIGURATION FILE opt = 1 moredetail optad = 1 moredetailad optcvad = 0
==> treePL2769972_100.out <== setting NLOPT parallel : LD_MMA you may want to set the plsimaniter > 100000 result: 4 final: 3046957.5 diff: 280371.75 best: 1(0) bestad: 1 (1) bestcv: 0 (0) PLACE THE LINES BELOW IN THE CONFIGURATION FILE opt = 1 optad = 1 moredetailad optcvad = 0
==> treePL2769972_1000.out <== setting NLOPT parallel : LD_MMA you may want to set the plsimaniter > 100000 result: 4 final: 3149824.2 diff: 254039.98 best: 1(0) bestad: 1 (1) bestcv: 3 (0) PLACE THE LINES BELOW IN THE CONFIGURATION FILE opt = 1 optad = 1 moredetailad optcvad = 3
==> treePL2769972_10000.out <== final: 3333963.1 diff: 95658.855 setting NLOPT parallel : LD_MMA you may want to set the plsimaniter > 100000 result: 4 final: 3164714.8 diff: 264907.15 best: 1(0) bestad: 1 (0) bestcv: 3 (0) PLACE THE LINES BELOW IN THE CONFIGURATION FILE opt = 1 optad = 1 optcvad = 3
Hi, This would also help me! I don't find much documentation about it. Thank you, Bests, Luana
