DoRun question
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Daniel Gates
May 14, 2012, 2:31:27 PM5/14/12
to treevo-discuss
Greetings all,
First off sorry for the slow response after our meeting Friday, I've
been trying to run the TreEvo code I have currently on the Mac in our
lab but it seems to be running into the same hang ups that my Linux
netbook (R version 2.10) and my Linux desktop (R version 2.14) have
been running into, in that it seems to get stuck in the calculation
step (mostly in the 'successes attempts expected number of attempts'
step, but sometimes even before that when the 'Calculating initial
simulations...' is the only stage its reached). I tried varying most
of the parameters like the size of the initial simulations, the tree
years, number of particles etc... but it always seems to get hung up.
While I was working on that I went ahead and just started to go
through the DoRun code line by line to see what the object looked like
and what was passed where and when. By removing the for (try in 1:
maxTries) and while(!run.goingwell) commands at the beginning I've
been able to walk through the initial steps but when I get to the
plsResult object on line 247 of the code at:
https://github.com/danjgates/TreEvo-Code/blob/master/TreEvoExample_trial1.R
it gives me this error:
> Error in if (crossprod(a - a.old) < tol) break :
missing value where TRUE/FALSE needed
I'm not sure what's going on but I can't proceed much further without
that, is this a result of me running the code without higher level for
and while loops at the beginning?
Thanks!
-Dan
First off sorry for the slow response after our meeting Friday, I've
been trying to run the TreEvo code I have currently on the Mac in our
lab but it seems to be running into the same hang ups that my Linux
netbook (R version 2.10) and my Linux desktop (R version 2.14) have
been running into, in that it seems to get stuck in the calculation
step (mostly in the 'successes attempts expected number of attempts'
step, but sometimes even before that when the 'Calculating initial
simulations...' is the only stage its reached). I tried varying most
of the parameters like the size of the initial simulations, the tree
years, number of particles etc... but it always seems to get hung up.
While I was working on that I went ahead and just started to go
through the DoRun code line by line to see what the object looked like
and what was passed where and when. By removing the for (try in 1:
maxTries) and while(!run.goingwell) commands at the beginning I've
been able to walk through the initial steps but when I get to the
plsResult object on line 247 of the code at:
https://github.com/danjgates/TreEvo-Code/blob/master/TreEvoExample_trial1.R
it gives me this error:
> Error in if (crossprod(a - a.old) < tol) break :
missing value where TRUE/FALSE needed
I'm not sure what's going on but I can't proceed much further without
that, is this a result of me running the code without higher level for
and while loops at the beginning?
Thanks!
-Dan
Brian O'Meara
May 14, 2012, 2:43:40 PM5/14/12
to treevo-...@googlegroups.com
Are the input arguments to pls (trueFreeValues and summaryValues) correct?
I've also made you a branch of your own to use. It's treevo/pkg-dgates-branch .
Brian
_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info
Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar: http://www.brianomeara.info/calendars/omeara
I've also made you a branch of your own to use. It's treevo/pkg-dgates-branch .
Brian
_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info
Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar: http://www.brianomeara.info/calendars/omeara
Daniel Gates
May 14, 2012, 6:05:05 PM5/14/12
to treevo-discuss
Going through the code I had it didn't raise any errors or warnings
when I made the objects for the two arguments (trueFreeValues and
summaryValues) and the values objects that I'm giving the pls()
function are as follows:
> trueFreeValues
[,1] [,2] [,3]
result.1 6.901255 0.0053949920 0
result.2 7.471981 0.0779871503 0
result.3 8.992336 0.0499939984 0
result.4 6.351811 0.0063076174 0
result.5 6.589194 0.0127002032 0
result.6 8.214607 0.1135017226 0
result.7 8.584603 0.0525883990 0
result.8 9.922737 0.0867378411 0
result.9 8.431663 0.0136035080 0
result.10 8.092588 0.0008841655 0
> summaryValues
[,1] [,2] [,3] [,4]
[,5]
result.1 1.130880e-15 3.376065e-15 4.131507e+40 1.297635e-15
4.171733e-17
result.2 1.751536e-15 1.802991e-15 9.952813e+40 1.978356e-15
2.572327e-17
result.3 1.648400e-15 2.484782e-15 8.878797e+40 1.859194e-15
3.231833e-17
result.4 1.154747e-15 3.373164e-15 4.322157e+40 1.298070e-15
4.177951e-17
result.5 1.357933e-15 3.289697e-15 6.065935e+40 1.554799e-15
4.062852e-17
result.6 1.766948e-15 1.686614e-15 1.011629e+41 2.019836e-15
2.000499e-17
result.7 1.617117e-15 2.647075e-15 8.560218e+40 1.857437e-15
3.080075e-17
result.8 1.876199e-15 8.666451e-16 1.129593e+41 2.154281e-15
8.164822e-18
result.9 1.346733e-15 3.299042e-15 5.964558e+40 1.547361e-15
4.048237e-17
result.10 8.341063e-16 3.385219e-15 2.055409e+40 9.580777e-16
4.188287e-17
[,6] [,7] [,8] [,9] [,
10]
result.1 1.1537673 3.692492e+39 7.810710e-14 2.195610e-14
2.258077e-16
result.2 0.1550800 8.501409e+39 1.129163e-13 1.927858e-14
2.866622e-17
result.3 0.4133570 7.575460e+39 1.090670e-13 1.847283e-14
1.615502e-16
result.4 0.1467045 3.695129e+39 7.946404e-14 2.197300e-14
1.395951e-16
result.5 0.6036012 5.359930e+39 9.182673e-14 2.166991e-14
1.570674e-16
result.6 0.6374087 8.830502e+39 1.146723e-13 1.818112e-14
5.300443e-17
result.7 0.9483783 7.562034e+39 1.073128e-13 1.822698e-14
2.041950e-16
result.8 0.8633707 9.919322e+39 1.222593e-13 6.001542e-15
2.311067e-16
result.9 1.0436138 5.308837e+39 9.078201e-14 2.180080e-14
9.813324e-17
result.10 1.0612009 1.864731e+39 5.960979e-14 2.201056e-14
2.360069e-16
[,11] [,12] [,13] [,14] [,
15]
result.1 6.310889e+40 5.924074e-14 3.222316e-15 9.210076e-16 3.124979e
+40
result.2 1.479398e+41 8.584839e-14 1.417583e-15 1.114735e-16 7.277451e
+40
result.3 1.372475e+41 8.290237e-14 2.430199e-15 7.061494e-16 6.755229e
+40
result.4 6.586039e+40 6.017858e-14 3.217941e-15 5.208825e-16 3.247230e
+40
result.5 9.315840e+40 6.961712e-14 3.140921e-15 5.866889e-16 4.583370e
+40
result.6 1.529121e+41 8.729957e-14 1.343604e-15 1.957223e-16 7.539652e
+40
result.7 1.324719e+41 8.154535e-14 2.634390e-15 9.210067e-16 6.519347e
+40
result.8 1.750442e+41 9.312864e-14 1.033272e-15 9.210075e-16 8.624231e
+40
result.9 9.070287e+40 6.908030e-14 3.140779e-15 4.428791e-16 4.502454e
+40
result.10 3.098418e+40 4.514152e-14 3.229526e-15 9.210075e-16 1.543871e
+40
[,16] [,17] [,18] [,19] [,20]
result.1 1.503376e-16 1.522065e+31 40.57147 0.03655095 1.683353e+13
result.2 2.231837e-16 3.090114e+31 58.99300 0.03008469 1.387101e+13
result.3 2.188174e-16 2.989520e+31 61.72814 0.02923706 1.326225e+13
result.4 1.530463e-16 1.575095e+31 33.70770 0.03846139 1.400661e+13
result.5 1.800390e-16 2.129122e+31 35.63492 0.03683572 1.355949e+13
result.6 2.278127e-16 3.197454e+31 44.93933 0.02934303 9.525695e+12
result.7 2.201406e-16 3.019936e+31 71.20279 0.03020271 1.163505e+13
result.8 2.566207e-16 3.879595e+31 60.95935 0.02535321 3.395329e+12
result.9 1.795474e-16 2.118657e+31 54.53427 0.03302850 2.154863e+13
result.10 1.155879e-16 8.942108e+30 53.70670 0.03465801 2.345611e+13
[,21] [,22] [,23] [,24] [,
25] [,26]
result.1 1.393746e-14 1.567703 2.893840e-10 0.07205184 2.439953e+13
9659124
result.2 1.017879e-14 1.636374 2.730735e-10 0.04878637 4.402187e+13
11407618
result.3 1.086817e-14 1.650661 4.110589e-10 0.03814837 3.242088e+13
10881906
result.4 1.392871e-14 1.532792 3.243276e-10 0.08192638 1.941658e+13
8482186
result.5 1.364432e-14 1.549543 2.528343e-10 0.08144571 1.895326e+13
8278701
result.6 9.345013e-15 1.592611 1.416921e-10 0.08016953 2.200213e+13
14622825
result.7 1.066937e-14 1.705085 2.282616e-10 0.06116795 2.810606e+13
7595645
result.8 3.060331e-15 1.655765 2.990147e-11 0.05929127 6.887658e+12
4992042
result.9 1.365508e-14 1.623967 1.616695e-10 0.05108313 2.937606e+13
11243819
result.10 1.397060e-14 1.624206 1.767332e-10 0.05842957 2.899408e+13
10629228
[,27] [,28] [,29] [,30] [,31]
[,32]
result.1 3.496395e-05 0.012309223 0.008917985 2.557414 0.3282450
0.11415430
result.2 1.862231e-05 0.007256307 0.004985087 2.963853 0.3215127
0.13476749
result.3 1.768462e-05 0.008787510 0.005990495 2.840069 0.2644075
0.07860288
result.4 4.180235e-05 0.013357243 0.009754620 2.461677 0.3501405
0.12867892
result.5 3.992777e-05 0.012990205 0.009391813 2.538347 0.3545094
0.13357162
result.6 3.177454e-05 0.013227816 0.008622642 2.782882 0.2923719
0.10040356
result.7 2.020333e-05 0.007510857 0.005193851 3.011405 0.2677742
0.07983508
result.8 8.436919e-06 0.006147663 0.004167227 3.091624 0.3077786
0.11353861
result.9 2.877034e-05 0.010214807 0.007315855 2.742458 0.3088067
0.10036589
result.10 2.632771e-05 0.010101044 0.007273100 2.758843 0.3009598
0.09659980
[,33] [,34] [,35] [,36] [,37] [,38] [,
39]
result.1 12.91085 5.489515 167.4356 4.747475 1.562301 1.425128
0.1889754
result.2 13.17946 5.931549 188.8744 5.348962 1.696289 1.528948
0.1585831
result.3 13.89431 5.963708 196.0066 5.414033 1.641429 1.486892
0.1887332
result.4 12.06084 5.166619 149.1888 4.315412 1.535277 1.404974
0.1965913
result.5 12.54467 5.384563 157.8791 4.512474 1.533805 1.403979
0.1825870
result.6 10.27603 4.709899 110.0903 3.849502 1.609498 1.467180
0.1493329
result.7 16.61063 6.870613 258.2889 6.278080 1.707836 1.531351
0.1341170
result.8 14.27328 6.249201 213.4056 5.243780 1.678675 1.501352
0.1295921
result.9 14.27634 6.003373 197.8505 5.282220 1.609330 1.455184
0.1518352
result.10 14.08686 5.932872 195.6238 5.267787 1.618340 1.464788
0.1639005
[,40] [,41] [,42]
result.1 0.14363791 0.01834340 0.02162805
result.2 0.11822339 0.02060747 0.02281620
result.3 0.14523788 0.00869667 0.01027602
result.4 0.15129269 0.02325969 0.02715795
result.5 0.13712675 0.02350262 0.02744103
result.6 0.10773552 0.01576513 0.01942535
result.7 0.09679663 0.01020611 0.01213742
result.8 0.09008832 0.02425720 0.02910902
result.9 0.11188833 0.01464798 0.01737958
result.10 0.12191448 0.01349673 0.01611042
when I made the objects for the two arguments (trueFreeValues and
summaryValues) and the values objects that I'm giving the pls()
function are as follows:
> trueFreeValues
[,1] [,2] [,3]
result.1 6.901255 0.0053949920 0
result.2 7.471981 0.0779871503 0
result.3 8.992336 0.0499939984 0
result.4 6.351811 0.0063076174 0
result.5 6.589194 0.0127002032 0
result.6 8.214607 0.1135017226 0
result.7 8.584603 0.0525883990 0
result.8 9.922737 0.0867378411 0
result.9 8.431663 0.0136035080 0
result.10 8.092588 0.0008841655 0
> summaryValues
[,1] [,2] [,3] [,4]
[,5]
result.1 1.130880e-15 3.376065e-15 4.131507e+40 1.297635e-15
4.171733e-17
result.2 1.751536e-15 1.802991e-15 9.952813e+40 1.978356e-15
2.572327e-17
result.3 1.648400e-15 2.484782e-15 8.878797e+40 1.859194e-15
3.231833e-17
result.4 1.154747e-15 3.373164e-15 4.322157e+40 1.298070e-15
4.177951e-17
result.5 1.357933e-15 3.289697e-15 6.065935e+40 1.554799e-15
4.062852e-17
result.6 1.766948e-15 1.686614e-15 1.011629e+41 2.019836e-15
2.000499e-17
result.7 1.617117e-15 2.647075e-15 8.560218e+40 1.857437e-15
3.080075e-17
result.8 1.876199e-15 8.666451e-16 1.129593e+41 2.154281e-15
8.164822e-18
result.9 1.346733e-15 3.299042e-15 5.964558e+40 1.547361e-15
4.048237e-17
result.10 8.341063e-16 3.385219e-15 2.055409e+40 9.580777e-16
4.188287e-17
[,6] [,7] [,8] [,9] [,
10]
result.1 1.1537673 3.692492e+39 7.810710e-14 2.195610e-14
2.258077e-16
result.2 0.1550800 8.501409e+39 1.129163e-13 1.927858e-14
2.866622e-17
result.3 0.4133570 7.575460e+39 1.090670e-13 1.847283e-14
1.615502e-16
result.4 0.1467045 3.695129e+39 7.946404e-14 2.197300e-14
1.395951e-16
result.5 0.6036012 5.359930e+39 9.182673e-14 2.166991e-14
1.570674e-16
result.6 0.6374087 8.830502e+39 1.146723e-13 1.818112e-14
5.300443e-17
result.7 0.9483783 7.562034e+39 1.073128e-13 1.822698e-14
2.041950e-16
result.8 0.8633707 9.919322e+39 1.222593e-13 6.001542e-15
2.311067e-16
result.9 1.0436138 5.308837e+39 9.078201e-14 2.180080e-14
9.813324e-17
result.10 1.0612009 1.864731e+39 5.960979e-14 2.201056e-14
2.360069e-16
[,11] [,12] [,13] [,14] [,
15]
result.1 6.310889e+40 5.924074e-14 3.222316e-15 9.210076e-16 3.124979e
+40
result.2 1.479398e+41 8.584839e-14 1.417583e-15 1.114735e-16 7.277451e
+40
result.3 1.372475e+41 8.290237e-14 2.430199e-15 7.061494e-16 6.755229e
+40
result.4 6.586039e+40 6.017858e-14 3.217941e-15 5.208825e-16 3.247230e
+40
result.5 9.315840e+40 6.961712e-14 3.140921e-15 5.866889e-16 4.583370e
+40
result.6 1.529121e+41 8.729957e-14 1.343604e-15 1.957223e-16 7.539652e
+40
result.7 1.324719e+41 8.154535e-14 2.634390e-15 9.210067e-16 6.519347e
+40
result.8 1.750442e+41 9.312864e-14 1.033272e-15 9.210075e-16 8.624231e
+40
result.9 9.070287e+40 6.908030e-14 3.140779e-15 4.428791e-16 4.502454e
+40
result.10 3.098418e+40 4.514152e-14 3.229526e-15 9.210075e-16 1.543871e
+40
[,16] [,17] [,18] [,19] [,20]
result.1 1.503376e-16 1.522065e+31 40.57147 0.03655095 1.683353e+13
result.2 2.231837e-16 3.090114e+31 58.99300 0.03008469 1.387101e+13
result.3 2.188174e-16 2.989520e+31 61.72814 0.02923706 1.326225e+13
result.4 1.530463e-16 1.575095e+31 33.70770 0.03846139 1.400661e+13
result.5 1.800390e-16 2.129122e+31 35.63492 0.03683572 1.355949e+13
result.6 2.278127e-16 3.197454e+31 44.93933 0.02934303 9.525695e+12
result.7 2.201406e-16 3.019936e+31 71.20279 0.03020271 1.163505e+13
result.8 2.566207e-16 3.879595e+31 60.95935 0.02535321 3.395329e+12
result.9 1.795474e-16 2.118657e+31 54.53427 0.03302850 2.154863e+13
result.10 1.155879e-16 8.942108e+30 53.70670 0.03465801 2.345611e+13
[,21] [,22] [,23] [,24] [,
25] [,26]
result.1 1.393746e-14 1.567703 2.893840e-10 0.07205184 2.439953e+13
9659124
result.2 1.017879e-14 1.636374 2.730735e-10 0.04878637 4.402187e+13
11407618
result.3 1.086817e-14 1.650661 4.110589e-10 0.03814837 3.242088e+13
10881906
result.4 1.392871e-14 1.532792 3.243276e-10 0.08192638 1.941658e+13
8482186
result.5 1.364432e-14 1.549543 2.528343e-10 0.08144571 1.895326e+13
8278701
result.6 9.345013e-15 1.592611 1.416921e-10 0.08016953 2.200213e+13
14622825
result.7 1.066937e-14 1.705085 2.282616e-10 0.06116795 2.810606e+13
7595645
result.8 3.060331e-15 1.655765 2.990147e-11 0.05929127 6.887658e+12
4992042
result.9 1.365508e-14 1.623967 1.616695e-10 0.05108313 2.937606e+13
11243819
result.10 1.397060e-14 1.624206 1.767332e-10 0.05842957 2.899408e+13
10629228
[,27] [,28] [,29] [,30] [,31]
[,32]
result.1 3.496395e-05 0.012309223 0.008917985 2.557414 0.3282450
0.11415430
result.2 1.862231e-05 0.007256307 0.004985087 2.963853 0.3215127
0.13476749
result.3 1.768462e-05 0.008787510 0.005990495 2.840069 0.2644075
0.07860288
result.4 4.180235e-05 0.013357243 0.009754620 2.461677 0.3501405
0.12867892
result.5 3.992777e-05 0.012990205 0.009391813 2.538347 0.3545094
0.13357162
result.6 3.177454e-05 0.013227816 0.008622642 2.782882 0.2923719
0.10040356
result.7 2.020333e-05 0.007510857 0.005193851 3.011405 0.2677742
0.07983508
result.8 8.436919e-06 0.006147663 0.004167227 3.091624 0.3077786
0.11353861
result.9 2.877034e-05 0.010214807 0.007315855 2.742458 0.3088067
0.10036589
result.10 2.632771e-05 0.010101044 0.007273100 2.758843 0.3009598
0.09659980
[,33] [,34] [,35] [,36] [,37] [,38] [,
39]
result.1 12.91085 5.489515 167.4356 4.747475 1.562301 1.425128
0.1889754
result.2 13.17946 5.931549 188.8744 5.348962 1.696289 1.528948
0.1585831
result.3 13.89431 5.963708 196.0066 5.414033 1.641429 1.486892
0.1887332
result.4 12.06084 5.166619 149.1888 4.315412 1.535277 1.404974
0.1965913
result.5 12.54467 5.384563 157.8791 4.512474 1.533805 1.403979
0.1825870
result.6 10.27603 4.709899 110.0903 3.849502 1.609498 1.467180
0.1493329
result.7 16.61063 6.870613 258.2889 6.278080 1.707836 1.531351
0.1341170
result.8 14.27328 6.249201 213.4056 5.243780 1.678675 1.501352
0.1295921
result.9 14.27634 6.003373 197.8505 5.282220 1.609330 1.455184
0.1518352
result.10 14.08686 5.932872 195.6238 5.267787 1.618340 1.464788
0.1639005
[,40] [,41] [,42]
result.1 0.14363791 0.01834340 0.02162805
result.2 0.11822339 0.02060747 0.02281620
result.3 0.14523788 0.00869667 0.01027602
result.4 0.15129269 0.02325969 0.02715795
result.5 0.13712675 0.02350262 0.02744103
result.6 0.10773552 0.01576513 0.01942535
result.7 0.09679663 0.01020611 0.01213742
result.8 0.09008832 0.02425720 0.02910902
result.9 0.11188833 0.01464798 0.01737958
result.10 0.12191448 0.01349673 0.01611042
Brian O'Meara
May 15, 2012, 2:07:43 AM5/15/12
to treevo-...@googlegroups.com
What happens if you pass these to pls (I don't want to go through the
effort to convert print() output back to usable output)? My guess is
that it has something to do with column 7, 11, or one of the other big
values of summaryValues: those numbers are getting rather big for R to
deal with. For example:
> (3.692492e+39)+100==3.692492e+39
[1] TRUE
If I am looking at the code correctly, some of these large columns
correspond to AIC values: it's odd that 2K - 2*lnL is something so
large.
Brian
_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info
Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar: http://www.brianomeara.info/calendars/omeara
effort to convert print() output back to usable output)? My guess is
that it has something to do with column 7, 11, or one of the other big
values of summaryValues: those numbers are getting rather big for R to
deal with. For example:
> (3.692492e+39)+100==3.692492e+39
[1] TRUE
If I am looking at the code correctly, some of these large columns
correspond to AIC values: it's odd that 2K - 2*lnL is something so
large.
Brian
_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info
Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar: http://www.brianomeara.info/calendars/omeara
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