The urge to breed early: Similar responses to environmental conditions in short- and long-distance migrants during spring migration
R code
Georg Rüppel, Ommo Hüppop, Heiko Schmaljohann & Vera Brust
Minimum stopover duration
## Running MCMC with 4 parallel chains, with 3 thread(s) per chain...
##
## Chain 1 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 2 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 3 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 4 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 3 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 2 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 3 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 2 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 4 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 1 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 4 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 1 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 2 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 2 finished in 3.0 seconds.
## Chain 1 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 1 finished in 3.1 seconds.
## Chain 3 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 3 finished in 3.3 seconds.
## Chain 4 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 4 finished in 3.8 seconds.
##
## All 4 chains finished successfully.
## Mean chain execution time: 3.3 seconds.
## Total execution time: 3.9 seconds.## mean lower upper f rhat ess_bulk ess_tail
## b[1,1] 11.0903457 5.4113035 17.951254 1 1.0017828 4227 2358
## b[2,1] 17.6877547 10.5518373 25.789824 1 0.9999123 3628 2769
## b[3,1] 4.1892116 2.3199880 6.461490 1 1.0023045 4124 2870
## b[4,1] 0.6904926 0.1114299 1.616263 1 1.0024877 3208 2732
## b[5,1] 4.1388571 2.3247511 6.331265 1 1.0000834 4198 2792
## b[1,2] 11.5087079 6.4688607 17.452973 1 1.0022310 3227 2691
## b[2,2] 13.0084852 8.3258905 18.145453 1 1.0010145 3728 2674
## b[3,2] 4.3266484 2.9546199 5.891555 1 0.9999789 4337 2873
## b[4,2] 3.1021919 2.1240040 4.219345 1 1.0002575 3590 2068
## b[5,2] 4.3699095 1.6052572 7.924506 1 1.0002376 3020 2774
## mu[1] 5.0191716 0.6862893 11.270064 1 1.0029676 2564 2039
## mu[2] 6.3591451 2.2104520 10.463468 1 1.0014669 2174 1571
## sigma[1] 4.3658624 1.5598926 9.941620 1 1.0016609 2354 2695
## sigma[2] 2.3292987 1.2939312 3.870950 1 0.9998708 1896 2033
## phi 1.2786004 0.8672450 1.672700 1 1.0004187 2943 2831
Inspect model parameter convergence
Checking chains for convergence.
Departure relative to night length
## Running MCMC with 4 parallel chains, with 3 thread(s) per chain...
##
## Chain 1 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 2 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 3 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 4 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 1 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 3 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 1 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 3 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 4 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 2 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 4 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 2 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 1 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 1 finished in 2.2 seconds.
## Chain 3 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 3 finished in 2.5 seconds.
## Chain 2 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 2 finished in 2.7 seconds.
## Chain 4 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 4 finished in 2.9 seconds.
##
## All 4 chains finished successfully.
## Mean chain execution time: 2.6 seconds.
## Total execution time: 2.9 seconds.## mean lower upper f rhat ess_bulk ess_tail
## b[1,1] 0.90708315 0.8741960 0.9426960 1.00000 1.0005681 4054 2703
## b[2,1] 0.04329791 0.0128743 0.0746901 0.99100 1.0014412 3080 2648
## b[3,1] 0.18411134 0.1493970 0.2169920 1.00000 0.9999249 4515 2815
## b[4,1] 0.13032191 0.0926153 0.1670920 1.00000 1.0001684 4043 2830
## b[5,1] 0.16183025 0.1362390 0.1857840 1.00000 1.0013437 4356 3264
## b[1,2] 0.94920977 0.9189060 0.9776930 1.00000 1.0018159 4051 2818
## b[2,2] 0.15354951 0.0885950 0.2202440 1.00000 1.0012831 3541 2835
## b[3,2] 0.20383044 0.1752470 0.2354720 1.00000 1.0005053 4365 2905
## b[4,2] 0.16892702 0.1451700 0.1937480 1.00000 1.0001138 3954 3351
## b[5,2] 0.17934000 0.1064400 0.2602980 0.99975 0.9999066 3836 3584
## sigma 0.05190700 0.0377031 0.0656711 1.00000 1.0023953 1884 2015
## v 1.27651697 0.8752140 1.6893100 1.00000 1.0019411 1969 2128
Inspect model parameter convergence
Checking chains for convergence.
Multistate Model
## Running MCMC with 4 parallel chains, with 3 thread(s) per chain...
##
## Chain 2 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 3 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 1 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 4 Iteration: 1 / 2000 [ 0%] (Warmup)
## Chain 2 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 2 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 1 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 1 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 3 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 3 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 4 Iteration: 1000 / 2000 [ 50%] (Warmup)
## Chain 4 Iteration: 1001 / 2000 [ 50%] (Sampling)
## Chain 2 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 2 finished in 3515.3 seconds.
## Chain 3 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 3 finished in 3618.8 seconds.
## Chain 4 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 4 finished in 3654.5 seconds.
## Chain 1 Iteration: 2000 / 2000 [100%] (Sampling)
## Chain 1 finished in 3754.9 seconds.
##
## All 4 chains finished successfully.
## Mean chain execution time: 3635.9 seconds.
## Total execution time: 3755.5 seconds.## mean lower upper f rhat ess_bulk
## mean_psi[1] 0.08437252 0.0439415 0.1257970 1.00000 1.0015657 2813
## mean_psi[2] 0.07431467 0.0573016 0.0924179 1.00000 0.9997408 3328
## mean_psi[3] 0.22791648 0.1760350 0.2820320 1.00000 0.9995929 3190
## mean_psi[4] 0.37389451 0.2858020 0.4599920 1.00000 1.0012685 2841
## mean_psi[5] 0.15527992 0.0888603 0.2244240 1.00000 1.0008647 2799
## mu1[1] -2.43143650 -3.0066600 -1.8922200 1.00000 1.0015405 2813
## mu1[2] -2.53298410 -2.7907900 -2.2758700 1.00000 0.9997689 3328
## mu1[3] -1.22957582 -1.5434500 -0.9344060 1.00000 0.9995930 3190
## mu1[4] -0.52232277 -0.9158630 -0.1603730 0.98500 1.0012134 2841
## mu1[5] -1.73058522 -2.2333500 -1.1616400 1.00000 1.0008646 2799
## b_u1_l[1] 6.40118829 -8.9335100 21.7914000 0.75100 1.0008931 3818
## b_u1_l[2] 9.61406161 -4.0047700 22.6398000 0.87550 1.0015169 3697
## b_u1_l[3] 4.28448228 -9.9452400 18.2895000 0.69550 0.9994359 4135
## b_u1_l[4] 3.09490290 -12.3284000 19.1370000 0.63050 0.9999447 3398
## b_u1_l[5] -7.19067591 -23.2934000 8.7395700 0.76900 1.0002110 4382
## b_u1_q[1] -5.54818188 -20.8875000 9.1687200 0.72100 1.0008941 3992
## b_u1_q[2] -12.03756579 -24.0760000 -0.1721970 0.95500 1.0020762 4262
## b_u1_q[3] -11.43484349 -25.6090000 2.3604900 0.91350 1.0013399 3825
## b_u1_q[4] 1.57225218 -12.8970000 16.7739000 0.56800 1.0012511 4239
## b_u1_q[5] 4.05915517 -10.7982000 20.0100000 0.66550 0.9997284 3887
## b_v1_l[1] 5.99384267 -10.7700000 21.7063000 0.72250 1.0000229 3526
## b_v1_l[2] 7.25132919 -7.1420500 20.8087000 0.79750 0.9998429 3454
## b_v1_l[3] 7.87206085 -6.4842200 22.5379000 0.81175 1.0013486 3407
## b_v1_l[4] 11.21552501 -4.1620000 24.8916000 0.89850 1.0019624 3927
## b_v1_l[5] 7.37020486 -7.0439200 22.0587000 0.79425 1.0062711 3976
## b_v1_q[1] 8.26686455 -6.8449700 25.7752000 0.80375 1.0001686 3780
## b_v1_q[2] 4.76398683 -9.6319700 19.7689000 0.70225 1.0013072 3788
## b_v1_q[3] 2.11121024 -12.3047000 16.3724000 0.59025 1.0003861 4130
## b_v1_q[4] -10.04502867 -23.1225000 3.4585500 0.89700 1.0011525 3298
## b_v1_q[5] -8.32565409 -23.3526000 7.1966200 0.81950 1.0006241 4402
## b_p1[1] 0.05321837 -0.3478080 0.4668830 0.57950 1.0003833 3332
## b_p1[2] 0.35962635 0.1357770 0.5829440 0.99625 1.0008020 3033
## b_p1[3] 0.00449856 -0.2951810 0.3317870 0.50525 1.0009389 3650
## b_p1[4] -0.02915397 -0.4886840 0.4354950 0.53950 1.0028831 3054
## b_p1[5] -0.33231956 -0.7008940 0.0324338 0.93275 1.0017896 4108
## b_h1[1] 0.09519020 -0.4667660 0.6720500 0.58625 1.0004327 2844
## b_h1[2] -0.44152719 -0.7112590 -0.1870090 0.99800 0.9997231 3542
## b_h1[3] -0.17334074 -0.4765350 0.1091820 0.83275 1.0023944 3104
## b_h1[4] 0.04444568 -0.3777900 0.4819590 0.56550 1.0008107 3117
## b_h1[5] -0.90125838 -1.4261300 -0.3530420 0.99750 1.0012067 2868
## b_r1 -1.36828130 -2.0793600 -0.7039560 1.00000 1.0008693 3281
## mean_chi[1] 0.47586613 0.2809570 0.6735170 1.00000 1.0009914 3989
## mean_chi[2] 0.68652195 0.5751990 0.7981140 1.00000 1.0003538 3389
## mean_chi[3] 0.48983852 0.3656020 0.6148680 1.00000 1.0001250 3486
## mean_chi[4] 0.29070517 0.1533450 0.4140150 1.00000 1.0017861 3808
## mean_chi[5] 0.80850927 0.6924920 0.9418430 1.00000 1.0007105 3669
## mu2[1] -0.10304486 -0.9397200 0.7241360 0.57700 1.0010138 3989
## mu2[2] 0.80315848 0.2397320 1.2987700 0.99425 1.0004109 3389
## mu2[3] -0.04218510 -0.5511330 0.4678220 0.54275 1.0001217 3486
## mu2[4] -0.92475662 -1.5592800 -0.2404860 0.99500 1.0020347 3808
## mu2[5] 1.52636637 0.6580360 2.4472400 0.99875 1.0007105 3669
## b_u2_l -7.65381082 -22.0507000 6.0688300 0.81750 1.0019055 3676
## b_u2_q -5.71999876 -19.6989000 8.4956300 0.74050 1.0010432 4773
## b_v2_l 8.19166254 -6.0547800 21.9645000 0.83525 1.0017802 3945
## b_v2_q -2.57258239 -16.2801000 11.2441000 0.61025 1.0003850 3853
## pX_A 0.49818082 0.4023240 0.5849710 1.00000 1.0010071 3173
## pX_N 0.46095713 0.3745670 0.5458510 1.00000 1.0021763 4338
## pC_A 0.96599875 0.9137950 1.0000000 1.00000 1.0007370 1748
## pC_N 0.93999643 0.8707000 0.9999470 1.00000 1.0003504 2449
## Noff 99.00200000 83.0000000 113.0000000 1.00000 1.0004033 3358
## Nrel 0.53805434 0.4510870 0.6141300 1.00000 1.0004997 3358
## ess_tail
## mean_psi[1] 2510
## mean_psi[2] 2850
## mean_psi[3] 2951
## mean_psi[4] 2336
## mean_psi[5] 2467
## mu1[1] 2510
## mu1[2] 2850
## mu1[3] 2951
## mu1[4] 2336
## mu1[5] 2467
## b_u1_l[1] 2708
## b_u1_l[2] 2664
## b_u1_l[3] 2989
## b_u1_l[4] 2791
## b_u1_l[5] 2755
## b_u1_q[1] 2755
## b_u1_q[2] 2915
## b_u1_q[3] 2237
## b_u1_q[4] 2607
## b_u1_q[5] 2574
## b_v1_l[1] 2924
## b_v1_l[2] 2695
## b_v1_l[3] 2281
## b_v1_l[4] 2669
## b_v1_l[5] 2799
## b_v1_q[1] 2655
## b_v1_q[2] 2755
## b_v1_q[3] 2627
## b_v1_q[4] 2673
## b_v1_q[5] 2789
## b_p1[1] 2548
## b_p1[2] 3128
## b_p1[3] 2665
## b_p1[4] 2600
## b_p1[5] 2780
## b_h1[1] 2446
## b_h1[2] 2332
## b_h1[3] 2859
## b_h1[4] 3031
## b_h1[5] 2633
## b_r1 2403
## mean_chi[1] 2491
## mean_chi[2] 2916
## mean_chi[3] 2314
## mean_chi[4] 2671
## mean_chi[5] 2270
## mu2[1] 2491
## mu2[2] 2916
## mu2[3] 2314
## mu2[4] 2671
## mu2[5] 2270
## b_u2_l 2812
## b_u2_q 2285
## b_v2_l 2745
## b_v2_q 2738
## pX_A 2343
## pX_N 3215
## pC_A 1358
## pC_N 2096
## Noff 2946
## Nrel 2946Effects
Departure timing
Departure decision
Predict departure decision
Predicted probability for offshore flights for individuals with unknown routing.
Inspect model parameter convergence
Checking chains for convergence.
