Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Rest of Brain ~ Body Mass
OU Un-weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
35.0937340 |
6.0299857 |
0.0085234 |
0.0649782 |
8611.8647 |
30.1929017 |
40.6405504 |
prior |
-17.7202080 |
4.9446584 |
0.0069893 |
0.0982557 |
2532.5455 |
-26.7869443 |
-10.1532887 |
alpha |
3.0112156 |
4.1903372 |
0.0059231 |
0.3104779 |
182.1531 |
0.0443452 |
8.4652205 |
sigma^2 |
0.0948241 |
0.1305784 |
0.0001846 |
0.0117059 |
124.4320 |
0.0021275 |
0.2638584 |
shift number |
1.3026228 |
1.1294804 |
0.0015965 |
0.0192860 |
3429.8312 |
0.0000000 |
3.0000000 |
N theta |
2.3026228 |
1.1294804 |
0.0015965 |
0.0192860 |
3429.8312 |
1.0000000 |
4.0000000 |
root theta |
1.7827258 |
0.0872482 |
0.0001233 |
0.0029554 |
871.5519 |
1.6181396 |
1.9561358 |
root beta |
0.6365952 |
0.0266114 |
0.0000376 |
0.0009060 |
862.7057 |
0.5853532 |
0.6872355 |
all theta |
1.8511293 |
0.6545371 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.6227724 |
0.1992435 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
35.0392824 |
4.5948791 |
0.0064949 |
0.0761639 |
3639.5693 |
30.1469878 |
40.5747266 |
prior |
-17.1633009 |
4.9348755 |
0.0069755 |
0.0988879 |
2490.3829 |
-25.9686790 |
-10.1514070 |
alpha |
2.4245096 |
2.8645725 |
0.0040491 |
0.1765854 |
263.1541 |
0.0521792 |
7.4081067 |
sigma^2 |
0.0767684 |
0.0908343 |
0.0001284 |
0.0062350 |
212.2385 |
0.0019014 |
0.2338630 |
shift number |
1.2701074 |
1.1438839 |
0.0016169 |
0.0194881 |
3445.2968 |
0.0000000 |
3.0000000 |
N theta |
2.2701074 |
1.1438839 |
0.0016169 |
0.0194881 |
3445.2968 |
1.0000000 |
4.0000000 |
root theta |
1.7751165 |
0.0885335 |
0.0001251 |
0.0030382 |
849.1326 |
1.6009166 |
1.9523789 |
root beta |
0.6391139 |
0.0271911 |
0.0000384 |
0.0009071 |
898.5340 |
0.5869471 |
0.6924215 |
all theta |
1.8313309 |
0.6389266 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.6276917 |
0.1910389 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
35.1136970 |
2.5579851 |
0.0030558 |
0.0475565 |
2893.1841 |
30.1153025 |
40.5792956 |
prior |
-17.3707357 |
4.8374886 |
0.0057790 |
0.0797489 |
3679.5183 |
-26.2353334 |
-10.1527919 |
alpha |
2.4883053 |
2.6221166 |
0.0031325 |
0.1341058 |
382.3042 |
0.0584858 |
7.1128795 |
sigma^2 |
0.0783042 |
0.0805598 |
0.0000962 |
0.0051205 |
247.5177 |
0.0019579 |
0.2218412 |
shift number |
1.2927113 |
1.1249445 |
0.0013439 |
0.0167169 |
4528.4773 |
0.0000000 |
3.0000000 |
N theta |
2.2927113 |
1.1249445 |
0.0013439 |
0.0167169 |
4528.4773 |
1.0000000 |
4.0000000 |
root theta |
1.7789407 |
0.0883499 |
0.0001055 |
0.0025610 |
1190.0935 |
1.6084118 |
1.9534330 |
root beta |
0.6378374 |
0.0265910 |
0.0000318 |
0.0007850 |
1147.5760 |
0.5850746 |
0.6888699 |
all theta |
1.8429826 |
0.6467617 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.6250019 |
0.1963772 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
3.0112156 |
2.4245096 |
2.4883053 |
sigma squared |
0.0948241 |
0.0767684 |
0.0783042 |
stationary variance |
0.0157451 |
0.0158317 |
0.0157344 |
phylogenetic halflife |
0.2301885 |
0.2858917 |
0.2785619 |
phylogenetic half life in units of tree height |
0.0031531 |
0.0039162 |
0.0038158 |
OU Weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
34.9817404 |
34.0805196 |
0.0481730 |
0.2102461 |
26275.83766 |
30.1645086 |
40.9718681 |
prior |
-17.4475603 |
5.0030986 |
0.0070719 |
0.0952160 |
2760.94615 |
-26.3314566 |
-10.1604904 |
alpha |
2.4104040 |
2.5347325 |
0.0035829 |
0.2158898 |
137.84791 |
0.0996141 |
6.7482358 |
sigma^2 |
0.0759462 |
0.0787575 |
0.0001113 |
0.0145134 |
29.44729 |
0.0039144 |
0.2100656 |
shift number |
1.3282651 |
1.1795765 |
0.0016673 |
0.0206004 |
3278.68844 |
0.0000000 |
3.0000000 |
N theta |
2.3282651 |
1.1795765 |
0.0016673 |
0.0206004 |
3278.68844 |
1.0000000 |
4.0000000 |
root theta |
1.7829262 |
0.0887056 |
0.0001254 |
0.0029828 |
884.42628 |
1.6125958 |
1.9623709 |
root beta |
0.6363281 |
0.0304438 |
0.0000430 |
0.0009794 |
966.27086 |
0.5826177 |
0.6876583 |
all theta |
1.8603783 |
0.6456922 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.6196096 |
0.1963656 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
35.2581918 |
3.1166710 |
0.0044054 |
0.0677628 |
2115.43009 |
30.1449338 |
41.0102256 |
prior |
-17.7353482 |
4.9462905 |
0.0069916 |
0.0997299 |
2459.84792 |
-26.8515410 |
-10.1709847 |
alpha |
2.6838008 |
2.4766979 |
0.0035008 |
0.1901318 |
169.68223 |
0.1388916 |
7.6123205 |
sigma^2 |
0.0840199 |
0.0759003 |
0.0001073 |
0.0122242 |
38.55211 |
0.0053879 |
0.2318710 |
shift number |
1.3425088 |
1.1561857 |
0.0016343 |
0.0210889 |
3005.70931 |
0.0000000 |
3.0000000 |
N theta |
2.3425088 |
1.1561857 |
0.0016343 |
0.0210889 |
3005.70931 |
1.0000000 |
4.0000000 |
root theta |
1.7836321 |
0.0882633 |
0.0001248 |
0.0030532 |
835.67737 |
1.6115112 |
1.9562768 |
root beta |
0.6361178 |
0.0270232 |
0.0000382 |
0.0009401 |
826.24225 |
0.5840623 |
0.6882896 |
all theta |
1.8569272 |
0.6439409 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.6208193 |
0.1904165 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
35.2812900 |
2.6589546 |
0.0031765 |
0.0515555 |
2659.94061 |
30.1616298 |
40.9963255 |
prior |
-17.5213760 |
4.9272709 |
0.0058863 |
0.0834153 |
3489.16662 |
-26.6309811 |
-10.1597370 |
alpha |
2.4490592 |
2.6466302 |
0.0031617 |
0.1927261 |
188.58433 |
0.1026100 |
7.4990343 |
sigma^2 |
0.0766546 |
0.0816180 |
0.0000975 |
0.0123166 |
43.91285 |
0.0039715 |
0.2328824 |
shift number |
1.3489990 |
1.1444863 |
0.0013672 |
0.0168757 |
4599.37818 |
0.0000000 |
3.0000000 |
N theta |
2.3489990 |
1.1444863 |
0.0013672 |
0.0168757 |
4599.37818 |
1.0000000 |
4.0000000 |
root theta |
1.7846413 |
0.0868189 |
0.0001037 |
0.0025226 |
1184.53069 |
1.6147808 |
1.9586763 |
root beta |
0.6359932 |
0.0262720 |
0.0000314 |
0.0007701 |
1163.99060 |
0.5840369 |
0.6876032 |
all theta |
1.8581881 |
0.6461108 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.6201451 |
0.1929334 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
2.4104040 |
2.6838008 |
2.4490592 |
sigma squared |
0.0759462 |
0.0840199 |
0.0766546 |
stationary variance |
0.0157538 |
0.0156532 |
0.0156498 |
phylogenetic halflife |
0.2875647 |
0.2582707 |
0.2830259 |
phylogenetic half life in units of tree height |
0.0039391 |
0.0035378 |
0.0038769 |
BM
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
18.2775948 |
7.4803682 |
0.0105735 |
0.5631936 |
176.4130 |
15.7843822 |
20.4164477 |
prior |
0.6164713 |
0.2044164 |
0.0002889 |
0.0112881 |
327.9374 |
0.4440760 |
0.7061801 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0032838 |
0.0505091 |
0.0000714 |
0.0020181 |
626.3865 |
0.0008291 |
0.0019532 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
2.0113992 |
0.2309762 |
0.0003265 |
0.0119320 |
374.7224 |
1.5601547 |
2.4697285 |
root beta |
0.5573060 |
0.0603019 |
0.0000852 |
0.0020121 |
898.1489 |
0.4406410 |
0.6764485 |
all theta |
2.0113992 |
0.2309762 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5573060 |
0.0603019 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
18.3064079 |
7.3184538 |
0.0103447 |
0.5598556 |
170.8782 |
16.0688213 |
20.4153472 |
prior |
0.6237749 |
0.1850790 |
0.0002616 |
0.0096982 |
364.1915 |
0.4663646 |
0.7061923 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0029100 |
0.0376909 |
0.0000533 |
0.0013298 |
803.3977 |
0.0008499 |
0.0019774 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
2.0012299 |
0.2160071 |
0.0003053 |
0.0104336 |
428.6126 |
1.5771577 |
2.4281743 |
root beta |
0.5607403 |
0.0609605 |
0.0000862 |
0.0020502 |
884.0677 |
0.4467587 |
0.6751603 |
all theta |
2.0012299 |
0.2160071 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5607403 |
0.0609605 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
18.7783360 |
1.3500690 |
0.0016128 |
0.0278327 |
2352.8896 |
16.1364436 |
20.4158315 |
prior |
0.6284968 |
0.0834715 |
0.0000997 |
0.0032951 |
641.6917 |
0.4629641 |
0.7061923 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0013603 |
0.0002890 |
0.0000003 |
0.0000090 |
1035.1674 |
0.0008578 |
0.0019345 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
2.0101932 |
0.2202032 |
0.0002631 |
0.0091532 |
578.7599 |
1.5771642 |
2.4407832 |
root beta |
0.5584174 |
0.0584850 |
0.0000699 |
0.0015991 |
1337.5705 |
0.4467370 |
0.6754541 |
all theta |
2.0101932 |
0.2202032 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5584174 |
0.0584850 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
1.000000e-06 |
1.000000e-06 |
1.000000e-06 |
sigma squared |
3.283800e-03 |
2.910000e-03 |
1.360300e-03 |
stationary variance |
1.641894e+03 |
1.455002e+03 |
6.801678e+02 |
phylogenetic halflife |
6.931472e+05 |
6.931472e+05 |
6.931472e+05 |
phylogenetic half life in units of tree height |
9.494774e+03 |
9.494774e+03 |
9.494774e+03 |
Model Selection
Bayes Factors
OU un-weighted predictor |
0.0000000 |
0.2036888 |
-13.20949 |
OU weighted predictor |
-0.2036888 |
0.0000000 |
-13.41318 |
BM |
13.2094895 |
13.4131783 |
0.00000 |
Neocortex ~ Body Mass
OU Un-weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
32.8168851 |
325.3523158 |
0.4598873 |
2.4571315 |
17532.7883 |
23.2103516 |
45.1411171 |
prior |
-24.4030877 |
6.2068539 |
0.0087734 |
0.1341944 |
2139.3137 |
-35.5309484 |
-13.6087716 |
alpha |
0.1716046 |
0.8369939 |
0.0011831 |
0.0578385 |
209.4166 |
0.0000044 |
0.8436107 |
sigma^2 |
0.0084372 |
0.0391459 |
0.0000553 |
0.0028598 |
187.3763 |
0.0003062 |
0.0400217 |
shift number |
3.5202887 |
1.5232459 |
0.0021531 |
0.0325417 |
2191.0895 |
1.0000000 |
6.0000000 |
N theta |
4.5202887 |
1.5232459 |
0.0021531 |
0.0325417 |
2191.0895 |
2.0000000 |
7.0000000 |
root theta |
1.6313836 |
0.1631586 |
0.0002306 |
0.0074549 |
479.0057 |
1.3181201 |
1.9548490 |
root beta |
0.7629408 |
0.0503600 |
0.0000712 |
0.0024286 |
429.9871 |
0.6575935 |
0.8571897 |
all theta |
1.3251069 |
0.8957646 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7960448 |
0.1136990 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
34.7617046 |
7.5023820 |
0.0106047 |
0.1727186 |
1886.7743 |
22.2552417 |
45.0002571 |
prior |
-24.5015083 |
6.3791129 |
0.0090169 |
0.1516194 |
1770.1548 |
-36.1846758 |
-13.6001526 |
alpha |
0.3187654 |
1.1402167 |
0.0016117 |
0.0651448 |
306.3484 |
0.0000040 |
1.9669025 |
sigma^2 |
0.0129646 |
0.0430854 |
0.0000609 |
0.0026391 |
266.5399 |
0.0002867 |
0.0779887 |
shift number |
3.5402487 |
1.5478234 |
0.0021879 |
0.0354216 |
1909.4418 |
1.0000000 |
6.0000000 |
N theta |
4.5402487 |
1.5478234 |
0.0021879 |
0.0354216 |
1909.4418 |
2.0000000 |
7.0000000 |
root theta |
1.6256985 |
0.1594735 |
0.0002254 |
0.0070665 |
509.2962 |
1.3082366 |
1.9456518 |
root beta |
0.7663215 |
0.0528718 |
0.0000747 |
0.0028236 |
350.6163 |
0.6648005 |
0.8696241 |
all theta |
1.4345007 |
0.8570816 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7966503 |
0.1280298 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
35.9948247 |
4.7117431 |
0.0056288 |
0.1297377 |
1318.9570 |
27.2722514 |
45.8533264 |
prior |
-24.5317310 |
6.1340891 |
0.0073280 |
0.1147180 |
2859.1482 |
-35.6316553 |
-13.6113687 |
alpha |
0.0098306 |
0.0164825 |
0.0000197 |
0.0007413 |
494.4096 |
0.0000044 |
0.0264806 |
sigma^2 |
0.0009273 |
0.0006842 |
0.0000008 |
0.0000256 |
715.2035 |
0.0003999 |
0.0015633 |
shift number |
3.5703093 |
1.5090296 |
0.0018027 |
0.0277791 |
2950.9401 |
1.0000000 |
6.0000000 |
N theta |
4.5703093 |
1.5090296 |
0.0018027 |
0.0277791 |
2950.9401 |
2.0000000 |
7.0000000 |
root theta |
1.6290920 |
0.1649816 |
0.0001971 |
0.0065984 |
625.1631 |
1.3070906 |
1.9535991 |
root beta |
0.7646730 |
0.0490338 |
0.0000586 |
0.0025157 |
379.8992 |
0.6680403 |
0.8593100 |
all theta |
1.3535442 |
0.9228891 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7934831 |
0.1016272 |
NA |
NA |
NA |
NA |
NA |
Shifts




A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.
OU parameters
alpha |
0.1716046 |
0.3187654 |
0.0098306 |
sigma squared |
0.0084372 |
0.0129646 |
0.0009273 |
stationary variance |
0.0245834 |
0.0203356 |
0.0471645 |
phylogenetic halflife |
4.0392108 |
2.1744741 |
70.5089047 |
phylogenetic half life in units of tree height |
0.0553294 |
0.0297861 |
0.9658355 |
OU Weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
27.7299483 |
7.2727090 |
0.0102800 |
0.3319691 |
479.95107 |
18.1191079 |
45.5480671 |
prior |
-25.5238969 |
7.2465200 |
0.0102430 |
0.2043728 |
1257.22388 |
-39.1606209 |
-13.7117725 |
alpha |
1.9745880 |
1.2575676 |
0.0017776 |
0.0639144 |
387.13761 |
0.1682837 |
4.1813244 |
sigma^2 |
0.0791454 |
0.0386295 |
0.0000546 |
0.0095792 |
16.26233 |
0.0101921 |
0.1471391 |
shift number |
3.5076134 |
1.7655332 |
0.0024956 |
0.0484508 |
1327.85008 |
1.0000000 |
7.0000000 |
N theta |
4.5076134 |
1.7655332 |
0.0024956 |
0.0484508 |
1327.85008 |
2.0000000 |
8.0000000 |
root theta |
1.5983688 |
0.1599716 |
0.0002261 |
0.0058570 |
746.00240 |
1.3091754 |
1.9102546 |
root beta |
0.7810255 |
0.0784384 |
0.0001109 |
0.0027180 |
832.83177 |
0.6404256 |
0.9096880 |
all theta |
1.5037504 |
0.6343943 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.8314348 |
0.2018003 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
26.8093017 |
25.7970518 |
0.0364643 |
0.2287368 |
12719.44549 |
17.4827060 |
42.9254696 |
prior |
-25.0632333 |
6.9830689 |
0.0098706 |
0.1805274 |
1496.25721 |
-38.4131284 |
-14.0243474 |
alpha |
1.9492654 |
1.3485050 |
0.0019061 |
0.0738196 |
333.70466 |
0.4129059 |
4.8562957 |
sigma^2 |
0.0813729 |
0.0533122 |
0.0000754 |
0.0167145 |
10.17336 |
0.0241168 |
0.2133917 |
shift number |
3.3965606 |
1.7061457 |
0.0024116 |
0.0427553 |
1592.40296 |
1.0000000 |
7.0000000 |
N theta |
4.3965606 |
1.7061457 |
0.0024116 |
0.0427553 |
1592.40296 |
2.0000000 |
8.0000000 |
root theta |
1.5829906 |
0.1601966 |
0.0002264 |
0.0063977 |
626.99035 |
1.2700234 |
1.8832959 |
root beta |
0.7873342 |
0.0779077 |
0.0001101 |
0.0028171 |
764.81433 |
0.6397492 |
0.9140903 |
all theta |
1.4860431 |
0.6366793 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.8357730 |
0.2032378 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
27.4931909 |
6.7523610 |
0.0080666 |
0.2651818 |
648.37136 |
17.8932531 |
44.5848315 |
prior |
-25.1563465 |
7.0231426 |
0.0083900 |
0.1587772 |
1956.53108 |
-38.3626798 |
-13.7289268 |
alpha |
1.7700885 |
1.1364938 |
0.0013577 |
0.0498612 |
519.52864 |
0.1944426 |
3.9083460 |
sigma^2 |
0.0722819 |
0.0407478 |
0.0000487 |
0.0092439 |
19.43098 |
0.0101921 |
0.1513429 |
shift number |
3.4719725 |
1.7267705 |
0.0020628 |
0.0385442 |
2007.01300 |
1.0000000 |
7.0000000 |
N theta |
4.4719725 |
1.7267705 |
0.0020628 |
0.0385442 |
2007.01300 |
2.0000000 |
8.0000000 |
root theta |
1.5883577 |
0.1578281 |
0.0001885 |
0.0051290 |
946.88858 |
1.2879207 |
1.8932525 |
root beta |
0.7856376 |
0.0772600 |
0.0000923 |
0.0023906 |
1044.49521 |
0.6438340 |
0.9126602 |
all theta |
1.4912459 |
0.6334104 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.8340280 |
0.2015946 |
NA |
NA |
NA |
NA |
NA |
Shifts




A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.
OU parameters
alpha |
1.9745880 |
1.9492654 |
1.7700885 |
sigma squared |
0.0791454 |
0.0813729 |
0.0722819 |
stationary variance |
0.0200410 |
0.0208727 |
0.0204176 |
phylogenetic halflife |
0.3510338 |
0.3555941 |
0.3915890 |
phylogenetic half life in units of tree height |
0.0048085 |
0.0048709 |
0.0053640 |
BM
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
20.8715295 |
5.8345207 |
0.0082471 |
0.3297257 |
313.1157 |
18.3840937 |
22.8589064 |
prior |
0.5385952 |
0.1854439 |
0.0002621 |
0.0086007 |
464.8978 |
0.2897727 |
0.7061340 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0023161 |
0.0334421 |
0.0000473 |
0.0009781 |
1169.0522 |
0.0007949 |
0.0017988 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
1.7390091 |
0.2242857 |
0.0003170 |
0.0117307 |
365.5590 |
1.3267016 |
2.1903187 |
root beta |
0.7418696 |
0.0601616 |
0.0000850 |
0.0020899 |
828.6437 |
0.6237639 |
0.8507326 |
all theta |
1.7390091 |
0.2242857 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7418696 |
0.0601616 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
21.0961872 |
5.8271612 |
0.0082367 |
0.3416098 |
290.9734 |
18.9708934 |
22.8607812 |
prior |
0.5374127 |
0.1708326 |
0.0002415 |
0.0076535 |
498.2259 |
0.3308981 |
0.7057571 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0021657 |
0.0289035 |
0.0000409 |
0.0009220 |
982.7194 |
0.0007761 |
0.0017194 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
1.7551085 |
0.1884625 |
0.0002664 |
0.0083070 |
514.7030 |
1.3846736 |
2.1215177 |
root beta |
0.7354261 |
0.0512223 |
0.0000724 |
0.0015023 |
1162.4672 |
0.6354001 |
0.8339267 |
all theta |
1.7551085 |
0.1884625 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7354261 |
0.0512223 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
21.2581897 |
1.3037861 |
0.0015575 |
0.0242721 |
2885.3370 |
18.6966750 |
22.8616275 |
prior |
0.5448964 |
0.1197458 |
0.0001431 |
0.0049407 |
587.4213 |
0.3132632 |
0.7061011 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0012331 |
0.0002535 |
0.0000003 |
0.0000060 |
1807.7957 |
0.0007878 |
0.0017434 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
1.7437475 |
0.2079345 |
0.0002484 |
0.0086983 |
571.4539 |
1.3434474 |
2.1630782 |
root beta |
0.7393104 |
0.0548553 |
0.0000655 |
0.0014734 |
1386.1299 |
0.6306284 |
0.8450501 |
all theta |
1.7437475 |
0.2079345 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7393104 |
0.0548553 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
1.000000e-06 |
1.000000e-06 |
1.000000e-06 |
sigma squared |
2.316100e-03 |
2.165700e-03 |
1.233100e-03 |
stationary variance |
1.158037e+03 |
1.082865e+03 |
6.165456e+02 |
phylogenetic halflife |
6.931472e+05 |
6.931472e+05 |
6.931472e+05 |
phylogenetic half life in units of tree height |
9.494774e+03 |
9.494774e+03 |
9.494774e+03 |
Model Selection
Bayes Factors
OU un-weighted predictor |
0.000000 |
-3.995941 |
18.21388 |
OU weighted predictor |
3.995941 |
0.000000 |
22.20983 |
BM |
-18.213884 |
-22.209825 |
0.00000 |
Neocortex ~ Rest of Brain
OU Un-weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
41.8484663 |
968.1801624 |
1.3685281 |
2.5734017 |
141545.86190 |
35.7727162 |
51.5812024 |
prior |
-23.2532256 |
4.5627496 |
0.0064495 |
0.1013316 |
2027.51208 |
-31.5383428 |
-13.8553269 |
alpha |
2.1636622 |
1.7379749 |
0.0024566 |
0.1382129 |
158.12120 |
0.0062162 |
5.6566696 |
sigma^2 |
0.0472127 |
0.0363335 |
0.0000514 |
0.0098932 |
13.48773 |
0.0010836 |
0.1276905 |
shift number |
2.9008673 |
1.0744340 |
0.0015187 |
0.0220908 |
2365.57596 |
1.0000000 |
5.0000000 |
N theta |
3.9008673 |
1.0744340 |
0.0015187 |
0.0220908 |
2365.57596 |
2.0000000 |
6.0000000 |
root theta |
-0.6339715 |
0.2108443 |
0.0002980 |
0.0083834 |
632.53131 |
-1.0156088 |
-0.2434912 |
root beta |
1.2418326 |
0.0814384 |
0.0001151 |
0.0025560 |
1015.15219 |
1.1179615 |
1.3615942 |
all theta |
-0.7405324 |
0.6921804 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.2713242 |
0.1649926 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
43.8279981 |
6.5804940 |
0.0093016 |
0.1134002 |
3367.35852 |
35.5612005 |
51.2919730 |
prior |
-23.7055845 |
4.5388822 |
0.0064157 |
0.0925822 |
2403.49505 |
-32.5613466 |
-15.0578766 |
alpha |
3.3374555 |
1.8237175 |
0.0025778 |
0.1051125 |
301.02788 |
0.4217073 |
6.7914446 |
sigma^2 |
0.0754616 |
0.0370812 |
0.0000524 |
0.0065471 |
32.07837 |
0.0096908 |
0.1453442 |
shift number |
2.7738666 |
1.0584480 |
0.0014961 |
0.0201765 |
2752.00582 |
1.0000000 |
5.0000000 |
N theta |
3.7738666 |
1.0584480 |
0.0014961 |
0.0201765 |
2752.00582 |
2.0000000 |
6.0000000 |
root theta |
-0.6552091 |
0.1876256 |
0.0002652 |
0.0159671 |
138.08124 |
-1.0318872 |
-0.2518178 |
root beta |
1.2564397 |
0.0626718 |
0.0000886 |
0.0062666 |
100.01786 |
1.1307464 |
1.3691711 |
all theta |
-0.8135768 |
0.6943325 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.2883986 |
0.1660847 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
44.2063127 |
3.9656266 |
0.0047374 |
0.1018626 |
1515.63351 |
35.8230725 |
51.3585512 |
prior |
-23.5228093 |
4.4778750 |
0.0053494 |
0.0810203 |
3054.61546 |
-32.4301834 |
-14.9626555 |
alpha |
2.8489993 |
1.6936491 |
0.0020233 |
0.0919749 |
339.08457 |
0.2918139 |
6.1444828 |
sigma^2 |
0.0633741 |
0.0349860 |
0.0000418 |
0.0061284 |
32.59057 |
0.0079628 |
0.1317232 |
shift number |
2.8171182 |
1.0398971 |
0.0012423 |
0.0172423 |
3637.38195 |
1.0000000 |
5.0000000 |
N theta |
3.8171182 |
1.0398971 |
0.0012423 |
0.0172423 |
3637.38195 |
2.0000000 |
6.0000000 |
root theta |
-0.6374330 |
0.1974473 |
0.0002359 |
0.0085295 |
535.86534 |
-1.0119052 |
-0.2304020 |
root beta |
1.2526926 |
0.0729528 |
0.0000872 |
0.0026681 |
747.60055 |
1.1146628 |
1.3610931 |
all theta |
-0.7952536 |
0.7046166 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.2832230 |
0.1673607 |
NA |
NA |
NA |
NA |
NA |
Shifts




A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.
OU parameters
alpha |
2.1636622 |
3.3374555 |
2.8489993 |
sigma squared |
0.0472127 |
0.0754616 |
0.0633741 |
stationary variance |
0.0109104 |
0.0113053 |
0.0111222 |
phylogenetic halflife |
0.3203583 |
0.2076873 |
0.2432950 |
phylogenetic half life in units of tree height |
0.0043883 |
0.0028449 |
0.0033327 |
OU Weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
43.8979990 |
4.4951105 |
0.0063539 |
0.1397838 |
1034.11020 |
35.4665226 |
51.2292886 |
prior |
-23.8578417 |
4.8785533 |
0.0068959 |
0.1162950 |
1759.78704 |
-32.6891924 |
-13.9740455 |
alpha |
3.5254850 |
3.3528039 |
0.0047392 |
0.2360772 |
201.70103 |
0.2385005 |
9.6435901 |
sigma^2 |
0.0797647 |
0.0732062 |
0.0001035 |
0.0096366 |
57.70999 |
0.0058361 |
0.2125637 |
shift number |
2.8162541 |
1.0660587 |
0.0015069 |
0.0216442 |
2425.93778 |
1.0000000 |
5.0000000 |
N theta |
3.8162541 |
1.0660587 |
0.0015069 |
0.0216442 |
2425.93778 |
2.0000000 |
6.0000000 |
root theta |
-0.6657844 |
0.2274737 |
0.0003215 |
0.0088728 |
657.26922 |
-1.0893730 |
-0.1897840 |
root beta |
1.2472358 |
0.0712471 |
0.0001007 |
0.0028328 |
632.57222 |
1.0979957 |
1.3728979 |
all theta |
-0.7906672 |
0.7157514 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.2814128 |
0.1727140 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
39.8941116 |
1060.6268466 |
1.4992020 |
4.2083819 |
63517.72602 |
35.5189152 |
51.6070603 |
prior |
-23.5907037 |
4.7007118 |
0.0066445 |
0.0999258 |
2212.95041 |
-32.0702708 |
-14.0855715 |
alpha |
3.0880861 |
2.9184596 |
0.0041253 |
0.2036243 |
205.42261 |
0.1653919 |
8.6588482 |
sigma^2 |
0.0698243 |
0.0635938 |
0.0000899 |
0.0083592 |
57.87616 |
0.0037153 |
0.1950417 |
shift number |
2.8634029 |
1.0683404 |
0.0015101 |
0.0201095 |
2822.37812 |
1.0000000 |
5.0000000 |
N theta |
3.8634029 |
1.0683404 |
0.0015101 |
0.0201095 |
2822.37812 |
2.0000000 |
6.0000000 |
root theta |
-0.6804767 |
0.2052922 |
0.0002902 |
0.0178454 |
132.33971 |
-1.0563787 |
-0.2436789 |
root beta |
1.2460685 |
0.0660245 |
0.0000933 |
0.0058992 |
125.26233 |
1.1226679 |
1.3698521 |
all theta |
-0.8217033 |
0.6744663 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.2899395 |
0.1654361 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
44.1407053 |
4.0499875 |
0.0048382 |
0.1062974 |
1451.6504 |
35.7025606 |
51.4354126 |
prior |
-23.7346579 |
4.7996548 |
0.0057338 |
0.0949231 |
2556.6780 |
-32.4161028 |
-13.9690050 |
alpha |
3.3856772 |
3.4595838 |
0.0041329 |
0.2157652 |
257.0898 |
0.1605903 |
9.9835032 |
sigma^2 |
0.0761431 |
0.0742844 |
0.0000887 |
0.0086867 |
73.1277 |
0.0037153 |
0.2226821 |
shift number |
2.8347433 |
1.0601508 |
0.0012665 |
0.0179683 |
3481.1499 |
1.0000000 |
5.0000000 |
N theta |
3.8347433 |
1.0601508 |
0.0012665 |
0.0179683 |
3481.1499 |
2.0000000 |
6.0000000 |
root theta |
-0.6680813 |
0.2048490 |
0.0002447 |
0.0091215 |
504.3520 |
-1.0502625 |
-0.2483801 |
root beta |
1.2471524 |
0.0672071 |
0.0000803 |
0.0031225 |
463.2499 |
1.1173492 |
1.3699408 |
all theta |
-0.7952818 |
0.7000289 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.2827302 |
0.1707245 |
NA |
NA |
NA |
NA |
NA |
Shifts




A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.
OU parameters
alpha |
3.5254850 |
3.0880861 |
3.3856772 |
sigma squared |
0.0797647 |
0.0698243 |
0.0761431 |
stationary variance |
0.0113126 |
0.0113054 |
0.0112449 |
phylogenetic halflife |
0.1966104 |
0.2244585 |
0.2047293 |
phylogenetic half life in units of tree height |
0.0026932 |
0.0030746 |
0.0028044 |
BM
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
17.5150011 |
3.6378668 |
0.0051421 |
0.1257875 |
836.4088 |
15.0151934 |
19.2080224 |
prior |
0.0165669 |
0.3883399 |
0.0005489 |
0.0257268 |
227.8525 |
-0.7030907 |
0.6884311 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0018120 |
0.0205364 |
0.0000290 |
0.0004406 |
2172.3401 |
0.0009041 |
0.0020257 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
-0.0609930 |
0.3097906 |
0.0004379 |
0.0224731 |
190.0242 |
-0.6826560 |
0.5377753 |
root beta |
1.0859743 |
0.0786945 |
0.0001112 |
0.0037377 |
443.2905 |
0.9333284 |
1.2395857 |
all theta |
-0.0609930 |
0.3097906 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.0859743 |
0.0786945 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
17.3634726 |
3.4730740 |
0.0049092 |
0.1065983 |
1061.5174 |
14.3767024 |
19.2089078 |
prior |
0.0313275 |
0.4147713 |
0.0005863 |
0.0287710 |
207.8292 |
-0.7075689 |
0.7059280 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0018395 |
0.0240165 |
0.0000339 |
0.0004343 |
3058.6033 |
0.0008981 |
0.0020419 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
-0.0887087 |
0.3567984 |
0.0005043 |
0.0288710 |
152.7290 |
-0.8569471 |
0.5581567 |
root beta |
1.0925840 |
0.0892841 |
0.0001262 |
0.0048934 |
332.9064 |
0.9224502 |
1.2750628 |
all theta |
-0.0887087 |
0.3567984 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.0925840 |
0.0892841 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
17.6151197 |
1.3390684 |
0.0015997 |
0.0202266 |
4382.8985 |
14.9845493 |
19.2093645 |
prior |
0.0204465 |
0.3772335 |
0.0004507 |
0.0232925 |
262.2946 |
-0.6797911 |
0.7018271 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0014139 |
0.0002979 |
0.0000004 |
0.0000032 |
8523.5930 |
0.0008871 |
0.0020107 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
-0.0620764 |
0.3078858 |
0.0003678 |
0.0187659 |
269.1786 |
-0.6691354 |
0.5533120 |
root beta |
1.0860732 |
0.0779255 |
0.0000931 |
0.0031770 |
601.6116 |
0.9318730 |
1.2387710 |
all theta |
-0.0620764 |
0.3078858 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.0860732 |
0.0779255 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
1.000000e-06 |
1.000000e-06 |
1.000000e-06 |
sigma squared |
1.812000e-03 |
1.839500e-03 |
1.413900e-03 |
stationary variance |
9.059836e+02 |
9.197657e+02 |
7.069329e+02 |
phylogenetic halflife |
6.931472e+05 |
6.931472e+05 |
6.931472e+05 |
phylogenetic half life in units of tree height |
9.494774e+03 |
9.494774e+03 |
9.494774e+03 |
Model Selection
Bayes Factors
OU un-weighted predictor |
0.000000 |
9.287355 |
-5.080023 |
OU weighted predictor |
-9.287355 |
0.000000 |
-14.367379 |
BM |
5.080023 |
14.367379 |
0.000000 |
Cerebellum ~ Body Mass
OU Un-weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
36.4566292 |
5.2871738 |
0.0074734 |
0.1968457 |
721.43166 |
26.6512833 |
44.8588394 |
prior |
-22.6710409 |
5.6442399 |
0.0079782 |
0.1343198 |
1765.75752 |
-35.4633553 |
-13.5989196 |
alpha |
3.3967852 |
5.9438755 |
0.0084017 |
0.5952794 |
99.70060 |
0.0038035 |
9.9937069 |
sigma^2 |
0.1050424 |
0.2063346 |
0.0002917 |
0.0338398 |
37.17824 |
0.0010685 |
0.2946486 |
shift number |
2.6200347 |
1.2740112 |
0.0018008 |
0.0261663 |
2370.62251 |
0.0000000 |
5.0000000 |
N theta |
3.6200347 |
1.2740112 |
0.0018008 |
0.0261663 |
2370.62251 |
1.0000000 |
6.0000000 |
root theta |
1.0382549 |
0.1167466 |
0.0001650 |
0.0061941 |
355.25057 |
0.8001524 |
1.2559433 |
root beta |
0.7520156 |
0.0388820 |
0.0000550 |
0.0022372 |
302.06664 |
0.6811840 |
0.8329248 |
all theta |
0.9931324 |
0.6417818 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7950026 |
0.2009048 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
36.4622926 |
5.0899284 |
0.0071946 |
0.1642591 |
960.20555 |
27.1691024 |
44.0587734 |
prior |
-22.9663043 |
5.6445773 |
0.0079786 |
0.1368128 |
1702.19561 |
-35.4640343 |
-13.5986330 |
alpha |
3.9902225 |
5.2405207 |
0.0074075 |
0.5069369 |
106.86637 |
0.0019369 |
13.5508251 |
sigma^2 |
0.1188536 |
0.1542000 |
0.0002180 |
0.0398436 |
14.97788 |
0.0008494 |
0.3952444 |
shift number |
2.5623925 |
1.2276378 |
0.0017353 |
0.0245591 |
2498.71025 |
1.0000000 |
5.0000000 |
N theta |
3.5623925 |
1.2276378 |
0.0017353 |
0.0245591 |
2498.71025 |
2.0000000 |
6.0000000 |
root theta |
1.0432452 |
0.1097785 |
0.0001552 |
0.0056271 |
380.59146 |
0.8192346 |
1.2560838 |
root beta |
0.7507707 |
0.0363652 |
0.0000514 |
0.0019621 |
343.51663 |
0.6822760 |
0.8259890 |
all theta |
1.0150288 |
0.6476237 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7856301 |
0.2000887 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
36.6716941 |
4.8719617 |
0.0058202 |
0.1620806 |
903.53652 |
27.0331859 |
44.7378321 |
prior |
-22.4925545 |
5.6129220 |
0.0067054 |
0.1150156 |
2381.57458 |
-35.6923940 |
-13.5974380 |
alpha |
3.0593154 |
4.3930424 |
0.0052481 |
0.3765281 |
136.12444 |
0.0033618 |
8.4583884 |
sigma^2 |
0.0899002 |
0.1297257 |
0.0001550 |
0.0294812 |
19.36251 |
0.0008476 |
0.2364548 |
shift number |
2.6073349 |
1.2534005 |
0.0014973 |
0.0219005 |
3275.45712 |
0.0000000 |
5.0000000 |
N theta |
3.6073349 |
1.2534005 |
0.0014973 |
0.0219005 |
3275.45712 |
1.0000000 |
6.0000000 |
root theta |
1.0458358 |
0.1124104 |
0.0001343 |
0.0049341 |
519.04028 |
0.8172568 |
1.2596879 |
root beta |
0.7494989 |
0.0372117 |
0.0000445 |
0.0017705 |
441.74762 |
0.6808556 |
0.8273908 |
all theta |
1.0080017 |
0.6410605 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7891335 |
0.1974405 |
NA |
NA |
NA |
NA |
NA |
Shifts




A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.
OU parameters
alpha |
3.3967852 |
3.9902225 |
3.0593154 |
sigma squared |
0.1050424 |
0.1188536 |
0.0899002 |
stationary variance |
0.0154620 |
0.0148931 |
0.0146929 |
phylogenetic halflife |
0.2040598 |
0.1737114 |
0.2265694 |
phylogenetic half life in units of tree height |
0.0027952 |
0.0023795 |
0.0031036 |
OU Weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
34.0371561 |
16.9841906 |
0.0240072 |
0.1725718 |
9686.12060 |
23.4572121 |
45.0021240 |
prior |
-43.0414028 |
17.3366744 |
0.0245055 |
0.5320266 |
1061.85433 |
-74.6248220 |
-13.6006896 |
alpha |
0.0862955 |
0.4436760 |
0.0006271 |
0.0475792 |
86.95550 |
0.0000168 |
0.1818922 |
sigma^2 |
0.0031725 |
0.0132612 |
0.0000187 |
0.0030428 |
18.99399 |
0.0003987 |
0.0053736 |
shift number |
7.7708516 |
4.0149894 |
0.0056752 |
0.1203739 |
1112.51084 |
1.0000000 |
15.0000000 |
N theta |
8.7708516 |
4.0149894 |
0.0056752 |
0.1203739 |
1112.51084 |
2.0000000 |
16.0000000 |
root theta |
1.0471759 |
0.1539052 |
0.0002175 |
0.0043775 |
1236.10923 |
0.7245957 |
1.3450879 |
root beta |
0.7434921 |
0.0493741 |
0.0000698 |
0.0012742 |
1501.54666 |
0.6455499 |
0.8458869 |
all theta |
0.9581601 |
0.8701998 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.8192586 |
0.4168436 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
36.2193168 |
5.3442745 |
0.0075542 |
0.2045992 |
682.29093 |
26.1425057 |
45.0325194 |
prior |
-27.3900948 |
11.1956702 |
0.0158251 |
0.4123270 |
737.25312 |
-51.1514961 |
-10.1458263 |
alpha |
4.2963449 |
6.6751439 |
0.0094354 |
0.5421482 |
151.59515 |
0.0003357 |
17.6570872 |
sigma^2 |
0.1248236 |
0.1804488 |
0.0002551 |
0.0381314 |
22.39451 |
0.0004158 |
0.5436612 |
shift number |
3.6037271 |
2.7171061 |
0.0038406 |
0.1007678 |
727.05938 |
0.0000000 |
10.0000000 |
N theta |
4.6037271 |
2.7171061 |
0.0038406 |
0.1007678 |
727.05938 |
1.0000000 |
11.0000000 |
root theta |
1.0294418 |
0.1260774 |
0.0001782 |
0.0050066 |
634.13821 |
0.7858762 |
1.2785029 |
root beta |
0.7534692 |
0.0426523 |
0.0000603 |
0.0017945 |
564.94620 |
0.6713536 |
0.8382244 |
all theta |
0.9896406 |
0.7275289 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.8054296 |
0.2992028 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
35.3269162 |
5.7027183 |
0.0068126 |
0.2043558 |
778.73515 |
24.5540173 |
45.3901024 |
prior |
-36.6378793 |
16.7264913 |
0.0199819 |
0.5212416 |
1029.74934 |
-71.0768777 |
-13.5984721 |
alpha |
2.1458487 |
5.8823090 |
0.0070272 |
0.4698360 |
156.74839 |
0.0000168 |
13.8846515 |
sigma^2 |
0.0621376 |
0.1604863 |
0.0001917 |
0.0324137 |
24.51429 |
0.0003820 |
0.4285442 |
shift number |
6.0538573 |
4.0295435 |
0.0048138 |
0.1279281 |
992.15559 |
1.0000000 |
14.0000000 |
N theta |
7.0538573 |
4.0295435 |
0.0048138 |
0.1279281 |
992.15559 |
2.0000000 |
15.0000000 |
root theta |
1.0395540 |
0.1418021 |
0.0001694 |
0.0037238 |
1450.07772 |
0.7542402 |
1.3213660 |
root beta |
0.7471385 |
0.0462549 |
0.0000553 |
0.0011885 |
1514.76778 |
0.6541054 |
0.8395345 |
all theta |
0.9645586 |
0.8295112 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.8174347 |
0.3907971 |
NA |
NA |
NA |
NA |
NA |
Shifts




A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.
OU parameters
alpha |
0.0862955 |
4.2963449 |
2.1458487 |
sigma squared |
0.0031725 |
0.1248236 |
0.0621376 |
stationary variance |
0.0183817 |
0.0145267 |
0.0144786 |
phylogenetic halflife |
8.0322527 |
0.1613342 |
0.3230177 |
phylogenetic half life in units of tree height |
0.1100263 |
0.0022100 |
0.0044247 |
BM
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
26.5485381 |
5.0509005 |
0.0071395 |
0.2360795 |
457.7421 |
24.1094743 |
28.3620457 |
prior |
0.6108970 |
0.1417179 |
0.0002003 |
0.0051922 |
744.9891 |
0.4426606 |
0.7061943 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0017322 |
0.0289745 |
0.0000410 |
0.0006944 |
1741.0983 |
0.0006316 |
0.0014304 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
1.2015515 |
0.1875839 |
0.0002652 |
0.0084088 |
497.6499 |
0.8415834 |
1.5800614 |
root beta |
0.6993194 |
0.0499740 |
0.0000706 |
0.0015356 |
1059.1323 |
0.6016079 |
0.8002787 |
all theta |
1.2015515 |
0.1875839 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.6993194 |
0.0499740 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
26.5629428 |
5.4926810 |
0.0077639 |
0.2882235 |
363.1700 |
24.2528337 |
28.3631810 |
prior |
0.6183126 |
0.1445437 |
0.0002043 |
0.0057300 |
636.3396 |
0.4722565 |
0.7062234 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0018346 |
0.0293708 |
0.0000415 |
0.0007758 |
1433.3601 |
0.0006274 |
0.0014132 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
1.1845039 |
0.1806239 |
0.0002553 |
0.0076412 |
558.7645 |
0.8240929 |
1.5464148 |
root beta |
0.7028933 |
0.0484279 |
0.0000685 |
0.0014403 |
1130.4657 |
0.6066532 |
0.7999328 |
all theta |
1.1845039 |
0.1806239 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7028933 |
0.0484279 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
26.7706289 |
1.2912353 |
0.0015425 |
0.0201380 |
4111.2956 |
24.2360618 |
28.3620457 |
prior |
0.6170407 |
0.0808391 |
0.0000966 |
0.0031029 |
678.7535 |
0.4545461 |
0.7062101 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0009983 |
0.0002071 |
0.0000002 |
0.0000036 |
3376.4739 |
0.0006390 |
0.0014160 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
1.1954987 |
0.1863705 |
0.0002226 |
0.0068648 |
737.0504 |
0.8428894 |
1.5792490 |
root beta |
0.7006512 |
0.0495059 |
0.0000591 |
0.0012905 |
1471.7183 |
0.6033083 |
0.8003800 |
all theta |
1.1954987 |
0.1863705 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.7006512 |
0.0495059 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
1.000000e-06 |
1.000000e-06 |
1.000000e-06 |
sigma squared |
1.732200e-03 |
1.834600e-03 |
9.983000e-04 |
stationary variance |
8.661245e+02 |
9.172910e+02 |
4.991699e+02 |
phylogenetic halflife |
6.931472e+05 |
6.931472e+05 |
6.931472e+05 |
phylogenetic half life in units of tree height |
9.494774e+03 |
9.494774e+03 |
9.494774e+03 |
Model Selection
Bayes Factors
OU un-weighted predictor |
0.00000 |
10.83171 |
22.78693 |
OU weighted predictor |
-10.83171 |
0.00000 |
11.95522 |
BM |
-22.78693 |
-11.95522 |
0.00000 |
Cerebellum ~ Rest of Brain
OU Un-weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
49.3269425 |
3.9357571 |
0.0055632 |
0.1012674 |
1510.4870 |
44.7023903 |
54.3961533 |
prior |
-20.9461595 |
4.7152885 |
0.0066651 |
0.1177747 |
1602.9213 |
-29.6111772 |
-13.8759109 |
alpha |
6.8740976 |
11.0784825 |
0.0156595 |
0.9947652 |
124.0279 |
0.2779672 |
25.3686391 |
sigma^2 |
0.1275789 |
0.2041039 |
0.0002885 |
0.0335094 |
37.0996 |
0.0070807 |
0.4817957 |
shift number |
1.8596786 |
0.9390306 |
0.0013273 |
0.0162547 |
3337.3617 |
1.0000000 |
4.0000000 |
N theta |
2.8596786 |
0.9390306 |
0.0013273 |
0.0162547 |
3337.3617 |
2.0000000 |
5.0000000 |
root theta |
-0.8119928 |
0.1345697 |
0.0001902 |
0.0081744 |
271.0109 |
-1.0893914 |
-0.5548172 |
root beta |
1.1142681 |
0.0367249 |
0.0000519 |
0.0017818 |
424.8286 |
1.0456704 |
1.1869901 |
all theta |
-0.8537486 |
0.5772799 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.1533021 |
0.1446264 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
49.2069385 |
24.8321423 |
0.0351004 |
0.2001908 |
15386.51547 |
44.7336228 |
54.3495102 |
prior |
-20.6981186 |
4.5007928 |
0.0063619 |
0.0991912 |
2058.88521 |
-28.9382894 |
-14.0955850 |
alpha |
5.7780187 |
9.4741714 |
0.0133918 |
0.8217482 |
132.92448 |
0.4593220 |
14.1225901 |
sigma^2 |
0.1065654 |
0.1706065 |
0.0002412 |
0.0373301 |
20.88682 |
0.0107418 |
0.2464464 |
shift number |
1.8447236 |
0.9458469 |
0.0013370 |
0.0161186 |
3443.38114 |
1.0000000 |
4.0000000 |
N theta |
2.8447236 |
0.9458469 |
0.0013370 |
0.0161186 |
3443.38114 |
2.0000000 |
5.0000000 |
root theta |
-0.8175726 |
0.1336386 |
0.0001889 |
0.0084307 |
251.26502 |
-1.0821132 |
-0.5492164 |
root beta |
1.1157420 |
0.0354847 |
0.0000502 |
0.0021581 |
270.34832 |
1.0438563 |
1.1854522 |
all theta |
-0.8297152 |
0.5830575 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.1484814 |
0.1445109 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
49.4082883 |
2.3190157 |
0.0027704 |
0.0330285 |
4929.79499 |
44.8529090 |
54.3869963 |
prior |
-20.2735808 |
4.0849296 |
0.0048800 |
0.0728433 |
3144.77495 |
-27.9431388 |
-13.9333419 |
alpha |
4.3403781 |
4.0391746 |
0.0048253 |
0.2440361 |
273.95365 |
0.3622365 |
11.2181190 |
sigma^2 |
0.0795458 |
0.0712826 |
0.0000852 |
0.0107704 |
43.80264 |
0.0077395 |
0.1954588 |
shift number |
1.8437600 |
0.9015113 |
0.0010770 |
0.0128477 |
4923.73617 |
1.0000000 |
4.0000000 |
N theta |
2.8437600 |
0.9015113 |
0.0010770 |
0.0128477 |
4923.73617 |
2.0000000 |
5.0000000 |
root theta |
-0.8121158 |
0.1336923 |
0.0001597 |
0.0071305 |
351.53857 |
-1.0924216 |
-0.5548172 |
root beta |
1.1143510 |
0.0354722 |
0.0000424 |
0.0018812 |
355.53859 |
1.0457706 |
1.1888983 |
all theta |
-0.8479819 |
0.5802528 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.1524684 |
0.1437857 |
NA |
NA |
NA |
NA |
NA |
Shifts




A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.
OU parameters
alpha |
6.8740976 |
5.7780187 |
4.3403781 |
sigma squared |
0.1275789 |
0.1065654 |
0.0795458 |
stationary variance |
0.0092797 |
0.0092216 |
0.0091635 |
phylogenetic halflife |
0.1008346 |
0.1199628 |
0.1596974 |
phylogenetic half life in units of tree height |
0.0013812 |
0.0016433 |
0.0021875 |
OU Weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
49.3481274 |
2.7736407 |
0.0039206 |
0.0517473 |
2872.9267 |
44.9024246 |
54.2997755 |
prior |
-19.6678169 |
4.1849779 |
0.0059155 |
0.0888331 |
2219.4042 |
-27.4896496 |
-13.7336059 |
alpha |
3.7221887 |
5.8580373 |
0.0082804 |
0.4490953 |
170.1482 |
0.0861110 |
11.8009314 |
sigma^2 |
0.0686369 |
0.1055998 |
0.0001493 |
0.0102375 |
106.4000 |
0.0016914 |
0.2156493 |
shift number |
1.8430573 |
0.9128674 |
0.0012903 |
0.0152115 |
3601.4190 |
1.0000000 |
4.0000000 |
N theta |
2.8430573 |
0.9128674 |
0.0012903 |
0.0152115 |
3601.4190 |
2.0000000 |
5.0000000 |
root theta |
-0.8220552 |
0.1245090 |
0.0001760 |
0.0076035 |
268.1453 |
-1.0632893 |
-0.5772153 |
root beta |
1.1169222 |
0.0329857 |
0.0000466 |
0.0019887 |
275.1177 |
1.0503486 |
1.1789120 |
all theta |
-0.8348596 |
0.5893023 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.1494329 |
0.1432998 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
49.2633328 |
11.9856559 |
0.0169418 |
0.1048105 |
13077.1885 |
44.4475506 |
54.6753513 |
prior |
-19.5913878 |
4.1938216 |
0.0059280 |
0.0836046 |
2516.2815 |
-27.3412844 |
-13.6981301 |
alpha |
3.0033150 |
3.1793302 |
0.0044940 |
0.1988068 |
255.7459 |
0.1220655 |
8.8839884 |
sigma^2 |
0.0554521 |
0.0580222 |
0.0000820 |
0.0047153 |
151.4141 |
0.0022603 |
0.1624690 |
shift number |
1.8739583 |
0.9437113 |
0.0013339 |
0.0160975 |
3436.8470 |
1.0000000 |
4.0000000 |
N theta |
2.8739583 |
0.9437113 |
0.0013339 |
0.0160975 |
3436.8470 |
2.0000000 |
5.0000000 |
root theta |
-0.8433433 |
0.1415927 |
0.0002001 |
0.0095398 |
220.2925 |
-1.1111085 |
-0.5703628 |
root beta |
1.1226095 |
0.0395323 |
0.0000559 |
0.0018656 |
449.0013 |
1.0502957 |
1.1927854 |
all theta |
-0.8553063 |
0.6042763 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.1545158 |
0.1485375 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
49.3834736 |
2.3793226 |
0.0028424 |
0.0377764 |
3967.0407 |
44.7301931 |
54.5654094 |
prior |
-19.5954467 |
4.1241172 |
0.0049268 |
0.0724996 |
3235.8677 |
-27.3738546 |
-13.7444268 |
alpha |
3.2850853 |
4.4575868 |
0.0053252 |
0.2784352 |
256.3016 |
0.0949506 |
9.8046308 |
sigma^2 |
0.0607616 |
0.0831734 |
0.0000994 |
0.0066471 |
156.5705 |
0.0017156 |
0.1805526 |
shift number |
1.8560947 |
0.9205252 |
0.0010997 |
0.0132498 |
4826.7162 |
1.0000000 |
4.0000000 |
N theta |
2.8560947 |
0.9205252 |
0.0010997 |
0.0132498 |
4826.7162 |
2.0000000 |
5.0000000 |
root theta |
-0.8378266 |
0.1351284 |
0.0001614 |
0.0074360 |
330.2258 |
-1.0776892 |
-0.5727548 |
root beta |
1.1210664 |
0.0361976 |
0.0000432 |
0.0020173 |
321.9858 |
1.0518719 |
1.1855103 |
all theta |
-0.8414627 |
0.5941776 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.1507620 |
0.1444982 |
NA |
NA |
NA |
NA |
NA |
Shifts




A shows the locations of the selection regimes on the phylogeny. B shows the optimum regression lines associated with each regime. C and D show the posterior distribution of \(\beta\) and \(\theta\) values associated with each regime.

Plot shows the median values for parameters associated with each selection regime, along with the posterior probability associeated with each regime. \(\theta\) is the intercept of the optimum regression line, and \(\beta\) is the coefficient of the predictor.
OU parameters
alpha |
3.7221887 |
3.0033150 |
3.2850853 |
sigma squared |
0.0686369 |
0.0554521 |
0.0607616 |
stationary variance |
0.0092200 |
0.0092318 |
0.0092481 |
phylogenetic halflife |
0.1862203 |
0.2307940 |
0.2109982 |
phylogenetic half life in units of tree height |
0.0025509 |
0.0031614 |
0.0028903 |
BM
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
27.7751952 |
2.4020119 |
0.0033953 |
0.0459851 |
2728.4557 |
25.2802762 |
29.4104014 |
prior |
0.3937618 |
0.2363242 |
0.0003340 |
0.0136611 |
299.2596 |
-0.0585239 |
0.7062204 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0010826 |
0.0120831 |
0.0000171 |
0.0001197 |
10198.0175 |
0.0006101 |
0.0013692 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
-0.5335550 |
0.2761243 |
0.0003903 |
0.0183661 |
226.0361 |
-1.0676802 |
0.0195057 |
root beta |
1.0371505 |
0.0694229 |
0.0000981 |
0.0031915 |
473.1717 |
0.9005716 |
1.1748000 |
all theta |
-0.5335550 |
0.2761243 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.0371505 |
0.0694229 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
27.7948634 |
2.2579275 |
0.0031916 |
0.0416064 |
2945.1048 |
25.2930660 |
29.4091996 |
prior |
0.4024882 |
0.2212113 |
0.0003127 |
0.0125847 |
308.9778 |
-0.0115160 |
0.7062136 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0010673 |
0.0121688 |
0.0000172 |
0.0000996 |
14925.6437 |
0.0006119 |
0.0013760 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
-0.5423194 |
0.2701564 |
0.0003819 |
0.0170906 |
249.8696 |
-1.0794213 |
-0.0185238 |
root beta |
1.0386770 |
0.0680850 |
0.0000962 |
0.0030871 |
486.4145 |
0.9043142 |
1.1715899 |
all theta |
-0.5423194 |
0.2701564 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.0386770 |
0.0680850 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
27.8347888 |
1.2748328 |
0.0015230 |
0.0145494 |
7677.4573 |
25.3257300 |
29.4090188 |
prior |
0.4060624 |
0.2165916 |
0.0002587 |
0.0117126 |
341.9621 |
-0.0058340 |
0.7061951 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0009620 |
0.0002027 |
0.0000002 |
0.0000010 |
37254.5836 |
0.0006154 |
0.0013760 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
-0.5446117 |
0.2660055 |
0.0003178 |
0.0144844 |
337.2734 |
-1.0719802 |
-0.0308299 |
root beta |
1.0392547 |
0.0673263 |
0.0000804 |
0.0025535 |
695.1869 |
0.9079109 |
1.1714135 |
all theta |
-0.5446117 |
0.2660055 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.0392547 |
0.0673263 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
1.000000e-06 |
1.000000e-06 |
1.000000e-06 |
sigma squared |
1.082600e-03 |
1.067300e-03 |
9.620000e-04 |
stationary variance |
5.412753e+02 |
5.336342e+02 |
4.809976e+02 |
phylogenetic halflife |
6.931472e+05 |
6.931472e+05 |
6.931472e+05 |
phylogenetic half life in units of tree height |
9.494774e+03 |
9.494774e+03 |
9.494774e+03 |
Model Selection
Bayes Factors
OU un-weighted predictor |
0.0000000 |
-0.1973664 |
-10.65050 |
OU weighted predictor |
0.1973664 |
0.0000000 |
-10.45313 |
BM |
10.6504986 |
10.4531321 |
0.00000 |
Medulla ~ Body Mass
OU Un-weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
41.5090395 |
3.8289470 |
0.0054122 |
0.1171954 |
1067.4259 |
35.8256584 |
49.7403512 |
prior |
-13.2359031 |
4.2147195 |
0.0059575 |
0.0975562 |
1866.4989 |
-21.1753098 |
-7.5672757 |
alpha |
3.3050082 |
3.6660083 |
0.0051819 |
0.2550397 |
206.6196 |
0.1363300 |
10.3375381 |
sigma^2 |
0.0480708 |
0.0487685 |
0.0000689 |
0.0043616 |
125.0206 |
0.0026400 |
0.1485004 |
shift number |
0.9079163 |
0.9474716 |
0.0013393 |
0.0188478 |
2527.0234 |
0.0000000 |
3.0000000 |
N theta |
1.9079163 |
0.9474716 |
0.0013393 |
0.0188478 |
2527.0234 |
1.0000000 |
4.0000000 |
root theta |
1.0677990 |
0.0784913 |
0.0001109 |
0.0023994 |
1070.1740 |
0.9133303 |
1.2251224 |
root beta |
0.5870589 |
0.0223279 |
0.0000316 |
0.0006535 |
1167.5238 |
0.5429637 |
0.6312144 |
all theta |
1.0574266 |
0.4913659 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5829843 |
0.1672830 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
41.3631024 |
266.9873493 |
0.3773881 |
0.7808967 |
116894.5314 |
36.3959447 |
51.5809923 |
prior |
-14.2426511 |
4.7314415 |
0.0066879 |
0.1238551 |
1459.3499 |
-22.8511111 |
-7.5456825 |
alpha |
4.6785248 |
6.8827947 |
0.0097289 |
0.5139241 |
179.3625 |
0.0000963 |
15.8941958 |
sigma^2 |
0.0683668 |
0.1023175 |
0.0001446 |
0.0100184 |
104.3035 |
0.0002943 |
0.2297625 |
shift number |
1.0391208 |
1.0308954 |
0.0014572 |
0.0225655 |
2087.0883 |
0.0000000 |
3.0000000 |
N theta |
2.0391208 |
1.0308954 |
0.0014572 |
0.0225655 |
2087.0883 |
1.0000000 |
4.0000000 |
root theta |
1.0785224 |
0.0819400 |
0.0001158 |
0.0026366 |
965.8252 |
0.9241345 |
1.2383921 |
root beta |
0.5848160 |
0.0231503 |
0.0000327 |
0.0007174 |
1041.1920 |
0.5402858 |
0.6285270 |
all theta |
1.0486085 |
0.5214857 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5846585 |
0.1845006 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
41.9231253 |
3.8363852 |
0.0045831 |
0.1238482 |
959.5443 |
36.1171349 |
51.0201071 |
prior |
-13.6856649 |
4.4820591 |
0.0053544 |
0.0951877 |
2217.1404 |
-22.0645257 |
-7.5456825 |
alpha |
3.7860633 |
5.5320481 |
0.0066087 |
0.3588624 |
237.6381 |
0.0000963 |
12.1936336 |
sigma^2 |
0.0551960 |
0.0811289 |
0.0000969 |
0.0067506 |
144.4347 |
0.0002899 |
0.1765419 |
shift number |
0.9848495 |
0.9948119 |
0.0011884 |
0.0179993 |
3054.7043 |
0.0000000 |
3.0000000 |
N theta |
1.9848495 |
0.9948119 |
0.0011884 |
0.0179993 |
3054.7043 |
1.0000000 |
4.0000000 |
root theta |
1.0745056 |
0.0792044 |
0.0000946 |
0.0020732 |
1459.4939 |
0.9194360 |
1.2309349 |
root beta |
0.5855490 |
0.0225094 |
0.0000269 |
0.0005687 |
1566.8394 |
0.5411605 |
0.6294026 |
all theta |
1.0552870 |
0.5152106 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5832427 |
0.1810461 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
3.3050082 |
4.6785248 |
3.7860633 |
sigma squared |
0.0480708 |
0.0683668 |
0.0551960 |
stationary variance |
0.0072724 |
0.0073064 |
0.0072894 |
phylogenetic halflife |
0.2097263 |
0.1481551 |
0.1830786 |
phylogenetic half life in units of tree height |
0.0028728 |
0.0020294 |
0.0025078 |
OU Weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
41.2835153 |
13.7754579 |
0.0194717 |
0.0830299 |
27525.98063 |
35.7122525 |
49.9597488 |
prior |
-13.6388157 |
4.3165686 |
0.0061015 |
0.0992767 |
1890.52593 |
-21.5471531 |
-7.5688246 |
alpha |
4.2604272 |
4.4098640 |
0.0062334 |
0.3547219 |
154.55194 |
0.1307626 |
13.0623479 |
sigma^2 |
0.0632336 |
0.0605777 |
0.0000856 |
0.0117015 |
26.80038 |
0.0029137 |
0.1846570 |
shift number |
0.8863359 |
0.9398395 |
0.0013285 |
0.0173897 |
2920.92708 |
0.0000000 |
3.0000000 |
N theta |
1.8863359 |
0.9398395 |
0.0013285 |
0.0173897 |
2920.92708 |
1.0000000 |
4.0000000 |
root theta |
1.0628151 |
0.0790345 |
0.0001117 |
0.0024745 |
1020.15246 |
0.9071124 |
1.2185394 |
root beta |
0.5884737 |
0.0227734 |
0.0000322 |
0.0006632 |
1179.28354 |
0.5447026 |
0.6336061 |
all theta |
1.0306371 |
0.4868995 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5931910 |
0.1673254 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
41.5112926 |
15.1526428 |
0.0214183 |
0.1079103 |
19717.46412 |
35.9587216 |
50.9632229 |
prior |
-14.8072017 |
4.5998722 |
0.0065019 |
0.1174755 |
1533.19221 |
-23.2159396 |
-7.6044929 |
alpha |
6.5957192 |
7.4787290 |
0.0105712 |
0.6444929 |
134.65402 |
0.1690026 |
21.1131089 |
sigma^2 |
0.0982441 |
0.1050929 |
0.0001485 |
0.0224355 |
21.94206 |
0.0035006 |
0.3049199 |
shift number |
0.9375865 |
0.9927251 |
0.0014032 |
0.0205929 |
2323.92104 |
0.0000000 |
3.0000000 |
N theta |
1.9375865 |
0.9927251 |
0.0014032 |
0.0205929 |
2323.92104 |
1.0000000 |
4.0000000 |
root theta |
1.0684390 |
0.0821825 |
0.0001162 |
0.0025050 |
1076.35167 |
0.9122302 |
1.2245628 |
root beta |
0.5873688 |
0.0235899 |
0.0000333 |
0.0006783 |
1209.47255 |
0.5432975 |
0.6302896 |
all theta |
1.0416593 |
0.4914309 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5890748 |
0.1662890 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
41.4593996 |
3.6096713 |
0.0043122 |
0.1089838 |
1097.01189 |
35.8481951 |
50.5724231 |
prior |
-14.1893126 |
4.5347975 |
0.0054174 |
0.0990316 |
2096.85432 |
-22.5942861 |
-7.5687857 |
alpha |
5.5380599 |
6.3335626 |
0.0075663 |
0.4609355 |
188.80603 |
0.1310891 |
17.7483074 |
sigma^2 |
0.0818695 |
0.0862560 |
0.0001030 |
0.0148852 |
33.57929 |
0.0029077 |
0.2550722 |
shift number |
0.9019543 |
0.9517985 |
0.0011370 |
0.0160179 |
3530.83604 |
0.0000000 |
3.0000000 |
N theta |
1.9019543 |
0.9517985 |
0.0011370 |
0.0160179 |
3530.83604 |
1.0000000 |
4.0000000 |
root theta |
1.0661482 |
0.0799066 |
0.0000955 |
0.0021172 |
1424.37666 |
0.9119163 |
1.2294966 |
root beta |
0.5878956 |
0.0222287 |
0.0000266 |
0.0005490 |
1639.57971 |
0.5433200 |
0.6319634 |
all theta |
1.0401616 |
0.4894724 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5901547 |
0.1660488 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
4.2604272 |
6.5957192 |
5.5380599 |
sigma squared |
0.0632336 |
0.0982441 |
0.0818695 |
stationary variance |
0.0074210 |
0.0074476 |
0.0073915 |
phylogenetic halflife |
0.1626943 |
0.1050905 |
0.1251607 |
phylogenetic half life in units of tree height |
0.0022286 |
0.0014395 |
0.0017145 |
BM
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
39.2152166 |
5.3639924 |
0.0075820 |
0.3038042 |
311.7373 |
36.7448552 |
41.1466455 |
prior |
0.6788686 |
0.1204073 |
0.0001702 |
0.0043025 |
783.1856 |
0.6330636 |
0.7062662 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0011216 |
0.0287079 |
0.0000406 |
0.0007992 |
1290.1996 |
0.0001907 |
0.0004964 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
1.1952786 |
0.1189474 |
0.0001681 |
0.0033782 |
1239.7808 |
0.9562364 |
1.4226816 |
root beta |
0.5441943 |
0.0294542 |
0.0000416 |
0.0006725 |
1918.4505 |
0.4873376 |
0.6020805 |
all theta |
1.1952786 |
0.1189474 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5441943 |
0.0294542 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
39.2401535 |
5.2602146 |
0.0074353 |
0.2921217 |
324.2496 |
36.7917790 |
41.1481149 |
prior |
0.6801823 |
0.1247115 |
0.0001763 |
0.0046029 |
734.0918 |
0.6372407 |
0.7062661 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0011499 |
0.0297980 |
0.0000421 |
0.0008503 |
1227.9455 |
0.0001909 |
0.0005005 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000 |
1.0000000 |
1.0000000 |
root theta |
1.1881919 |
0.1198608 |
0.0001694 |
0.0034659 |
1195.9835 |
0.9607080 |
1.4220706 |
root beta |
0.5460381 |
0.0290105 |
0.0000410 |
0.0006493 |
1996.5603 |
0.4887957 |
0.6019384 |
all theta |
1.1881919 |
0.1198608 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5460381 |
0.0290105 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
39.5398235 |
1.3237531 |
0.0015814 |
0.0206836 |
4096.012 |
36.9633492 |
41.1481359 |
prior |
0.6843679 |
0.0222519 |
0.0000266 |
0.0004679 |
2261.199 |
0.6398485 |
0.7062674 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0003298 |
0.0000817 |
0.0000001 |
0.0000019 |
1931.510 |
0.0001955 |
0.0004949 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.000 |
1.0000000 |
1.0000000 |
root theta |
1.1910668 |
0.1129721 |
0.0001350 |
0.0025704 |
1931.692 |
0.9652457 |
1.4101063 |
root beta |
0.5454135 |
0.0279189 |
0.0000334 |
0.0005067 |
3036.491 |
0.4910910 |
0.6011421 |
all theta |
1.1910668 |
0.1129721 |
NA |
NA |
NA |
NA |
NA |
all beta |
0.5454135 |
0.0279189 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
1.000000e-06 |
1.000000e-06 |
1.000000e-06 |
sigma squared |
1.121600e-03 |
1.149900e-03 |
3.298000e-04 |
stationary variance |
5.608190e+02 |
5.749726e+02 |
1.648884e+02 |
phylogenetic halflife |
6.931472e+05 |
6.931472e+05 |
6.931472e+05 |
phylogenetic half life in units of tree height |
9.494774e+03 |
9.494774e+03 |
9.494774e+03 |
Model Selection
Bayes Factors
OU un-weighted predictor |
0.000000 |
2.781395 |
10.203771 |
OU weighted predictor |
-2.781395 |
0.000000 |
7.422375 |
BM |
-10.203771 |
-7.422375 |
0.000000 |
Medulla ~ Brain - Medulla
OU Un-weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
1.7522090 |
3.7995359 |
0.0053707 |
0.0776254 |
2395.81636 |
-4.5470349 |
10.0104748 |
prior |
-22.4496164 |
7.5935414 |
0.0107335 |
0.1237780 |
3763.58437 |
-35.9808618 |
-7.5510880 |
alpha |
1.8312202 |
5.4169974 |
0.0076570 |
0.3958960 |
187.22117 |
0.0018216 |
5.2534384 |
sigma^2 |
0.1965629 |
0.5648455 |
0.0007984 |
0.0604427 |
87.33156 |
0.0016171 |
0.5731199 |
shift number |
3.2620115 |
1.8079498 |
0.0025555 |
0.0278850 |
4203.70457 |
0.0000000 |
6.0000000 |
N theta |
4.2620115 |
1.8079498 |
0.0025555 |
0.0278850 |
4203.70457 |
1.0000000 |
7.0000000 |
root theta |
0.0386984 |
0.1469366 |
0.0002077 |
0.0049100 |
895.55421 |
-0.2463257 |
0.3293682 |
root beta |
2.0211784 |
0.0989513 |
0.0001399 |
0.0033985 |
847.73257 |
1.8246235 |
2.2197310 |
all theta |
-0.0000263 |
0.5695715 |
NA |
NA |
NA |
NA |
NA |
all beta |
2.0143173 |
0.3559705 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
1.6152515 |
4.0382400 |
0.0057081 |
0.0762111 |
2807.6801 |
-4.7612341 |
9.9148239 |
prior |
-22.3536421 |
7.3950545 |
0.0104530 |
0.1184226 |
3899.5440 |
-35.5151023 |
-7.5568869 |
alpha |
1.6134493 |
2.4163646 |
0.0034155 |
0.1557324 |
240.7505 |
0.0077718 |
4.9349811 |
sigma^2 |
0.1748316 |
0.2657741 |
0.0003757 |
0.0228881 |
134.8354 |
0.0027762 |
0.5349240 |
shift number |
3.1977419 |
1.7763906 |
0.0025109 |
0.0261610 |
4610.7304 |
0.0000000 |
6.0000000 |
N theta |
4.1977419 |
1.7763906 |
0.0025109 |
0.0261610 |
4610.7304 |
1.0000000 |
7.0000000 |
root theta |
0.0328168 |
0.1477508 |
0.0002088 |
0.0050882 |
843.2126 |
-0.2506327 |
0.3332717 |
root beta |
2.0255728 |
0.0978225 |
0.0001383 |
0.0034046 |
825.5666 |
1.8298877 |
2.2177652 |
all theta |
-0.0096880 |
0.5575420 |
NA |
NA |
NA |
NA |
NA |
all beta |
2.0231221 |
0.3577688 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
1.7491591 |
3.8474998 |
0.0045963 |
0.0681550 |
3186.8492 |
-4.7366259 |
10.1403367 |
prior |
-22.3965279 |
7.5550059 |
0.0090254 |
0.1058632 |
5093.0693 |
-35.8767328 |
-7.5518260 |
alpha |
1.8112893 |
4.8132570 |
0.0057501 |
0.3052256 |
248.6772 |
0.0016737 |
5.1942068 |
sigma^2 |
0.1947053 |
0.5049689 |
0.0006033 |
0.0434987 |
134.7647 |
0.0015708 |
0.5593491 |
shift number |
3.2251050 |
1.8005597 |
0.0021510 |
0.0236563 |
5793.2264 |
0.0000000 |
6.0000000 |
N theta |
4.2251050 |
1.8005597 |
0.0021510 |
0.0236563 |
5793.2264 |
1.0000000 |
7.0000000 |
root theta |
0.0379746 |
0.1478402 |
0.0001766 |
0.0043464 |
1156.9536 |
-0.2504921 |
0.3326066 |
root beta |
2.0219536 |
0.0985401 |
0.0001177 |
0.0029649 |
1104.5665 |
1.8254760 |
2.2181488 |
all theta |
-0.0018032 |
0.5640189 |
NA |
NA |
NA |
NA |
NA |
all beta |
2.0164429 |
0.3569081 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
1.8312202 |
1.6134493 |
1.8112893 |
sigma squared |
0.1965629 |
0.1748316 |
0.1947053 |
stationary variance |
0.0536699 |
0.0541795 |
0.0537477 |
phylogenetic halflife |
0.3785166 |
0.4296058 |
0.3826816 |
phylogenetic half life in units of tree height |
0.0051849 |
0.0058848 |
0.0052420 |
OU Weighted Predictor
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
1.6870223 |
6.4239754 |
0.0090803 |
0.0806102 |
6350.79032 |
-4.5209183 |
9.7571172 |
prior |
-22.8214888 |
8.0430091 |
0.0113688 |
0.1381083 |
3391.54429 |
-37.1071472 |
-7.5475393 |
alpha |
0.8953529 |
0.7386092 |
0.0010440 |
0.0476398 |
240.37498 |
0.0050705 |
2.2895193 |
sigma^2 |
0.0937568 |
0.0717741 |
0.0001015 |
0.0233151 |
9.47674 |
0.0024696 |
0.2249473 |
shift number |
3.4919511 |
1.9689116 |
0.0027831 |
0.0335574 |
3442.50539 |
0.0000000 |
7.0000000 |
N theta |
4.4919511 |
1.9689116 |
0.0027831 |
0.0335574 |
3442.50539 |
1.0000000 |
8.0000000 |
root theta |
0.0248345 |
0.1556828 |
0.0002201 |
0.0053766 |
838.43474 |
-0.2825694 |
0.3339287 |
root beta |
2.0288008 |
0.1038741 |
0.0001468 |
0.0036624 |
804.42878 |
1.8130806 |
2.2263659 |
all theta |
-0.0130095 |
0.5930876 |
NA |
NA |
NA |
NA |
NA |
all beta |
2.0217922 |
0.3737887 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
1.8445543 |
15.6968246 |
0.0221875 |
0.1206296 |
16932.28259 |
-4.6937270 |
10.1958533 |
prior |
-22.7489227 |
8.3598458 |
0.0118167 |
0.1454702 |
3302.54166 |
-37.8490750 |
-7.5504050 |
alpha |
0.2823932 |
0.2564308 |
0.0003625 |
0.0173332 |
218.86754 |
0.0029359 |
0.7942673 |
sigma^2 |
0.0289217 |
0.0233267 |
0.0000330 |
0.0080629 |
8.36999 |
0.0024580 |
0.0803564 |
shift number |
3.7266799 |
2.0425844 |
0.0028872 |
0.0349737 |
3410.96417 |
0.0000000 |
7.0000000 |
N theta |
4.7266799 |
2.0425844 |
0.0028872 |
0.0349737 |
3410.96417 |
1.0000000 |
8.0000000 |
root theta |
0.0323440 |
0.1572310 |
0.0002222 |
0.0053410 |
866.63044 |
-0.2792059 |
0.3391053 |
root beta |
2.0226985 |
0.1046363 |
0.0001479 |
0.0036066 |
841.73636 |
1.8171688 |
2.2287718 |
all theta |
-0.0123135 |
0.6117893 |
NA |
NA |
NA |
NA |
NA |
all beta |
2.0166927 |
0.3750270 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
1.8177312 |
3.7712204 |
0.0045052 |
0.0766203 |
2422.56664 |
-4.6856370 |
10.0190088 |
prior |
-22.6661914 |
8.0869967 |
0.0096610 |
0.1176754 |
4722.84043 |
-37.1673859 |
-7.5519056 |
alpha |
0.6444566 |
0.6271871 |
0.0007493 |
0.0382279 |
269.17373 |
0.0031093 |
1.9495866 |
sigma^2 |
0.0673232 |
0.0619972 |
0.0000741 |
0.0187136 |
10.97568 |
0.0024284 |
0.2001058 |
shift number |
3.5607389 |
1.9872417 |
0.0023740 |
0.0286543 |
4809.74818 |
0.0000000 |
7.0000000 |
N theta |
4.5607389 |
1.9872417 |
0.0023740 |
0.0286543 |
4809.74818 |
1.0000000 |
8.0000000 |
root theta |
0.0266911 |
0.1558989 |
0.0001862 |
0.0045077 |
1196.11490 |
-0.2792444 |
0.3398225 |
root beta |
2.0273719 |
0.1044117 |
0.0001247 |
0.0031082 |
1128.44610 |
1.8109234 |
2.2274215 |
all theta |
-0.0158730 |
0.5957897 |
NA |
NA |
NA |
NA |
NA |
all beta |
2.0223107 |
0.3721234 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
0.8953529 |
0.2823932 |
0.6444566 |
sigma squared |
0.0937568 |
0.0289217 |
0.0673232 |
stationary variance |
0.0523574 |
0.0512082 |
0.0522326 |
phylogenetic halflife |
0.7741609 |
2.4545467 |
1.0755530 |
phylogenetic half life in units of tree height |
0.0106045 |
0.0336225 |
0.0147330 |
BM
Convergence

Plots show Gelman’s R statistics for log likelihood, \(\alpha\), and \(\sigma^2\). Solid lines indicate values Gelman’s R, and dashed lines indicate 95% CIs.
Likelihood

Plot shows the posterior probabilities of a shift occuring on each branch for each chain prior to merging.
Summary Statistics
chain1
lnL |
-3.1043191 |
4.9844194 |
0.0070455 |
0.3717504 |
179.77376 |
-5.6082686 |
-0.7790303 |
prior |
0.0007215 |
0.5969700 |
0.0008438 |
0.0597636 |
99.77721 |
-1.0837300 |
0.7060184 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0046895 |
0.0451218 |
0.0000638 |
0.0021074 |
458.45575 |
0.0016114 |
0.0040762 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
1.0000000 |
1.0000000 |
root theta |
0.5914128 |
0.3553966 |
0.0005024 |
0.0282264 |
158.53195 |
-0.1616797 |
1.2283366 |
root beta |
1.6128707 |
0.2279454 |
0.0003222 |
0.0230127 |
98.11330 |
1.2001830 |
2.0837462 |
all theta |
0.5914128 |
0.3553966 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.6128707 |
0.2279454 |
NA |
NA |
NA |
NA |
NA |
chain2
lnL |
-3.2260003 |
5.0025544 |
0.0070711 |
0.3792135 |
174.02681 |
-6.1554430 |
-0.7650817 |
prior |
-0.1125735 |
0.7441400 |
0.0010518 |
0.0877217 |
71.96071 |
-1.6193891 |
0.7055136 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0044840 |
0.0399889 |
0.0000565 |
0.0015834 |
637.79695 |
0.0015618 |
0.0042720 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
1.0000000 |
1.0000000 |
root theta |
0.6250258 |
0.4270128 |
0.0006036 |
0.0403877 |
111.78477 |
-0.2627850 |
1.4495799 |
root beta |
1.5974439 |
0.2674953 |
0.0003781 |
0.0315393 |
71.93302 |
1.0813234 |
2.1265179 |
all theta |
0.6250258 |
0.4270128 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.5974439 |
0.2674953 |
NA |
NA |
NA |
NA |
NA |
combined chains
lnL |
-2.8217676 |
1.4453849 |
0.0017267 |
0.0513652 |
791.82508 |
-5.6473066 |
-0.7748568 |
prior |
-0.0812564 |
0.6907863 |
0.0008252 |
0.0710773 |
94.45503 |
-1.4578125 |
0.7059570 |
alpha |
0.0000010 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
0.0000010 |
0.0000010 |
sigma^2 |
0.0027455 |
0.0006764 |
0.0000008 |
0.0000286 |
559.47729 |
0.0015901 |
0.0040769 |
shift number |
0.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
0.0000000 |
0.0000000 |
N theta |
1.0000000 |
0.0000000 |
0.0000000 |
0.0000000 |
0.00000 |
1.0000000 |
1.0000000 |
root theta |
0.6301677 |
0.3939463 |
0.0004706 |
0.0292737 |
181.10074 |
-0.2056259 |
1.3646437 |
root beta |
1.5939555 |
0.2496945 |
0.0002983 |
0.0232804 |
115.03656 |
1.1096241 |
2.1067321 |
all theta |
0.6301677 |
0.3939463 |
NA |
NA |
NA |
NA |
NA |
all beta |
1.5939555 |
0.2496945 |
NA |
NA |
NA |
NA |
NA |
Shifts
No shifts were detected with a posterior probability above the cutoff.
OU parameters
alpha |
1.000000e-06 |
1.000000e-06 |
1.000000e-06 |
sigma squared |
4.689500e-03 |
4.484000e-03 |
2.745500e-03 |
stationary variance |
2.344731e+03 |
2.241980e+03 |
1.372757e+03 |
phylogenetic halflife |
6.931472e+05 |
6.931472e+05 |
6.931472e+05 |
phylogenetic half life in units of tree height |
9.494774e+03 |
9.494774e+03 |
9.494774e+03 |
Model Selection
Bayes Factors
OU un-weighted predictor |
0.000000 |
-38.11658 |
3.868261 |
OU weighted predictor |
38.116580 |
0.00000 |
41.984840 |
BM |
-3.868261 |
-41.98484 |
0.000000 |