Hello all, I am running a BHM designed to estimate metabolism in streams. The model runs fine and converges with no errors. However, when I plot the parameters Rhat to see which days didn’t converge, I have 3 parameters that are doing well ( Pmax, alpha, and GPP, and two parameters that are not ( K600 and ER). I am not sure what changes do I need to make to make sure it all converges, and whether this is an acceptable estimation for the individual parameters based on the data or not. I am using 4 chains and 4000 steps divided between burning and saved steps.
I am following the convention of R^<1.1 and Neff/N <0.05 as not converged. But unsure what would be a realistic number. This is based on the mcmc diagnostic post. I would appreciate your suggestions and inputs on this.
My code is below the data , note that you need to install the StreamMetabolizer package as it has the stan models in it.
Sample data
solar.time DO.obs DO.sat depth temp.water light
4 12/10/2019 2:00 6.655733333 6.976690936 1 24.058 0
5 12/10/2019 3:00 6.562333333 6.983595513 1 24.11216667 0
6 12/10/2019 4:00 6.492533333 6.988034175 1 24.04183333 0.51835048
7 12/10/2019 5:00 6.437266667 6.992397346 1 23.99566667 16.82282922
8 12/10/2019 6:00 6.443466667 6.995071627 1 23.97216667 109.0053905
9 12/10/2019 7:00 6.4912 6.988502092 1 23.99616667 230.0909752
10 12/10/2019 8:00 6.5638 6.972060403 1 24.16016667 360.53043
11 12/10/2019 9:00 6.673466667 6.94862973 1 24.415 494.3776766
12 12/10/2019 10:00 6.769 6.912858625 1 24.66566667 601.2851976
13 12/10/2019 11:00 6.866333333 6.865479211 1 24.888 645.2566332
14 12/10/2019 12:00 7.001333333 6.84333908 1 25.53516667 653.9240514
15 12/10/2019 13:00 7.068133333 6.833110521 1 25.66366667 632.4809251
16 12/10/2019 14:00 6.943933333 6.839342204 1 24.9295 571.4659988
17 12/10/2019 15:00 6.82 6.868569657 1 24.76566667 474.6563439
18 12/10/2019 16:00 6.685133333 6.88236363 1 24.50416667 345.7230054
19 12/10/2019 17:00 6.595866667 6.887202158 1 24.50866667 192.5300489
20 12/10/2019 18:00 6.6732 6.889449107 1 24.65116667 54.26776106
21 12/10/2019 19:00 6.730933333 6.89152532 1 24.63166667 5.228815158
22 12/10/2019 20:00 6.7512 6.897608899 1 24.53366667 0.154055213
23 12/10/2019 21:00 6.720533333 6.907470176 1 24.44866667 0
24 12/10/2019 22:00 6.691066667 6.918683057 1 24.40666667 0
25 12/10/2019 23:00 6.648133333 6.930646595 1 24.3315 0
26 12/11/2019 0:00 6.542333333 6.943531903 1 24.24 0
27 12/11/2019 1:00 6.451733333 6.95355893 1 24.08233333 0
28 12/11/2019 2:00 6.366266667 6.961747224 1 24.1015 0
29 12/11/2019 3:00 6.2746 6.969466777 1 24.1205 0
30 12/11/2019 4:00 6.2352 6.974270675 1 24.06466667 0.851834705
31 12/11/2019 5:00 6.189333333 6.981318726 1 23.97833333 25.36700317
32 12/11/2019 6:00 6.144133333 6.986442004 1 23.929 118.3198405
33 12/11/2019 7:00 6.168533333 6.980936736 1 23.8925 253.1099957
34 12/11/2019 8:00 6.279933333 6.963584794 1 23.9915 390.6853785
35 12/11/2019 9:00 6.415133333 6.937932883 1 24.32233333 508.5933479
36 12/11/2019 10:00 6.598733333 6.90313412 1 24.63616667 596.4256619
37 12/11/2019 11:00 6.766666667 6.866664162 1 24.847 642.1850442
38 12/11/2019 12:00 6.8704 6.836731768 1 25.34766667 654.3803266
39 12/11/2019 13:00 7.059866667 6.801916304 1 25.44533333 637.7817837
40 12/11/2019 14:00 7.280933333 6.772938753 1 25.77416667 580.3341418
41 12/11/2019 15:00 7.4122 6.759026898 1 26.131 483.6173731
42 12/11/2019 16:00 7.536 6.75223179 1 26.04983333 356.9074138
43 12/11/2019 17:00 7.550066667 6.762705098 1 25.8285 214.9473478
44 12/11/2019 18:00 7.464533333 6.782658953 1 25.658 84.29810614
45 12/11/2019 19:00 7.3618 6.804711469 1 25.52566667 14.44947274
46 12/11/2019 20:00 7.227333333 6.827657684 1 25.3805 0.208427641
47 12/11/2019 21:00 7.1554 6.840908346 1 25.07466667 0
48 12/11/2019 22:00 7.112333333 6.853734007 1 25.0535 0
49 12/11/2019 23:00 7.059133333 6.86416114 1 25.1805 0
50 12/12/2019 0:00 7.052866667 6.869050804 1 24.94716667 0
51 12/12/2019 1:00 7.0544 6.879524341 1 24.89816667 0
52 12/12/2019 2:00 7.028933333 6.891851552 1 24.85366667 0
53 12/12/2019 3:00 6.9578 6.90434649 1 24.74633333 0.000453104
54 12/12/2019 4:00 6.8916 6.915867159 1 24.65666667 0.890348508
55 12/12/2019 5:00 6.771533333 6.925721964 1 24.52983333 26.10103095
56 12/12/2019 6:00 6.6448 6.934248621 1 24.60133333 119.8753451
57 12/12/2019 7:00 6.6236 6.934612651 1 24.4965 254.6102216
58 12/12/2019 8:00 6.674133333 6.928185677 1 24.46933333 392.7420156
59 12/12/2019 9:00 6.741933333 6.915472085 1 24.633 512.6178138
60 12/12/2019 10:00 6.851266667 6.887821264 1 24.83016667 595.4270216
61 12/12/2019 11:00 6.986666667 6.847113966 1 25.105 638.7002246
62 12/12/2019 12:00 7.109466667 6.804197392 1 25.59883333 651.0105954
63 12/12/2019 13:00 7.2276 6.764207033 1 26.00683333 629.6635271
64 12/12/2019 14:00 7.311466667 6.739516329 1 26.182 564.4805011
65 12/12/2019 15:00 7.2932 6.744727592 1 26.176 470.1339172
66 12/12/2019 16:00 7.2584 6.761423587 1 25.79633333 347.6088224
67 12/12/2019 17:00 7.199933333 6.78269958 1 25.23616667 192.8526586
68 12/12/2019 18:00 7.137866667 6.800226779 1 25.3265 73.98410965
69 12/12/2019 19:00 7.0986 6.804485501 1 25.21233333 13.58631044
70 12/12/2019 20:00 7.051733333 6.804561992 1 25.36966667 0.24014489
71 12/12/2019 21:00 6.9936 6.807477687 1 25.30433333 0
72 12/12/2019 22:00 6.921 6.814725263 1 25.2435 0.000453104
73 12/12/2019 23:00 6.8494 6.826930426 1 25.11566667 0.014499314
74 12/13/2019 0:00 6.8352 6.84104213 1 24.945 0.08382416
75 12/13/2019 1:00 6.8246 6.855039229 1 24.75233333 0.03171725
76 12/13/2019 2:00 6.8062 6.866954378 1 24.6005 0
77 12/13/2019 3:00 6.749066667 6.880585134 1 24.56383333 0
78 12/13/2019 4:00 6.6518 6.886595681 1 24.44 0.840507116
79 12/13/2019 5:00 6.558866667 6.888182176 1 24.267 25.04756516
80 12/13/2019 6:00 6.5318 6.886648647 1 24.54816667 117.2940141
81 12/13/2019 7:00 6.572466667 6.876539405 1 24.5725 252.6786411
82 12/13/2019 8:00 6.639 6.862793381 1 24.642 393.2195868
83 12/13/2019 9:00 6.6946 6.843578183 1 24.75533333 518.6472629
84 12/13/2019 10:00 6.739533333 6.809961233 1 25.04316667 607.4455937
85 12/13/2019 11:00 6.794933333 6.771278078 1 25.44283333 652.5158055
86 12/13/2019 12:00 6.875066667 6.73253818 1 25.88433333 662.3526839
87 12/13/2019 13:00 6.984133333 6.713714872 1 26.172 643.3644727
88 12/13/2019 14:00 7.100666667 6.715578279 1 26.01833333 584.3880594
89 12/13/2019 15:00 7.202733333 6.725715598 1 25.55483333 488.4501758
90 12/13/2019 16:00 7.239466667 6.744881443 1 25.438 363.2336458
91 12/13/2019 17:00 7.2002 6.75846441 1 25.4355 223.6559984
92 12/13/2019 18:00 7.103933333 6.767782158 1 25.321 91.05977066
93 12/13/2019 19:00 6.9964 6.77865411 1 25.21233333 16.11462834
94 12/13/2019 20:00 6.922866667 6.786462808 1 25.14516667 0.222020748
95 12/13/2019 21:00 6.9154 6.787171967 1 25.1255 0
96 12/13/2019 22:00 6.909866667 6.789037602 1 25.224 0
97 12/13/2019 23:00 6.892933333 6.791883405 1 25.16666667 0
98 12/14/2019 0:00 6.847066667 6.7988293 1 24.97433333 0
99 12/14/2019 1:00 6.772666667 6.811254411 1 24.87083333 0
100 12/14/2019 2:00 6.713 6.821255871 1 24.69483333 0
101 12/14/2019 3:00 6.671933333 6.829900483 1 24.66516667 0.001812414
102 12/14/2019 4:00 6.6642 6.833778578 1 24.56133333 0.927956104
103 12/14/2019 5:00 6.699866667 6.826438883 1 24.545 26.07656336
104 12/14/2019 6:00 6.750266667 6.813221288 1 24.83483333 116.5418621
105 12/14/2019 7:00 6.786733333 6.789284697 1 25.04383333 249.3492361
106 12/14/2019 8:00 6.794 6.75511343 1 25.26516667 387.1951217
107 12/14/2019 9:00 6.7712 6.718793939 1 25.54716667 508.6835155
108 12/14/2019 10:00 6.7578 6.687478513 1 26.0495 598.0609126
109 12/14/2019 11:00 6.781533333 6.665918921 1 26.22066667 638.7405508
110 12/14/2019 12:00 6.862066667 6.659343345 1 26.18383333 654.5624743
111 12/14/2019 13:00 6.933 6.664954917 1 26.02266667 631.9272325
112 12/14/2019 14:00 6.992333333 6.669483365 1 25.78933333 570.1592481
113 12/14/2019 15:00 7.0132 6.675241301 1 25.78283333 481.4592408
114 12/14/2019 16:00 7.015066667 6.675232691 1 25.73833333 359.0043771
115 12/14/2019 17:00 7.003933333 6.676907093 1 25.73233333 218.1281349
116 12/14/2019 18:00 6.983666667 6.681776888 1 25.68683333 87.80376843
117 12/14/2019 19:00 6.972133333 6.684438949 1 25.6455 15.26505916
118 12/14/2019 20:00 6.9348 6.689926882 1 25.62583333 0.126868999
119 12/14/2019 21:00 6.8738 6.695463839 1 25.637 0
120 12/14/2019 22:00 6.807733333 6.701460386 1 25.5185 0
121 12/14/2019 23:00 6.728 6.708831579 1 25.4165 0.000453104
122 12/15/2019 0:00 6.6376 6.713354219 1 25.36433333 0.011327589
123 12/15/2019 1:00 6.577533333 6.712890923 1 25.26466667 0.004531036
124 12/15/2019 2:00 6.512466667 6.7124065 1 25.4015 0
125 12/15/2019 3:00 6.464133333 6.709933903 1 25.30466667 0.000906207
126 12/15/2019 4:00 6.440266667 6.707993161 1 25.26866667 0.754870542
127 12/15/2019 5:00 6.451933333 6.706650898 1 25.28866667 22.02445816
128 12/15/2019 6:00 6.508333333 6.695885072 1 25.307 107.5758488
129 12/15/2019 7:00 6.587266667 6.680825207 1 25.60933333 235.9772437
130 12/15/2019 8:00 6.6696 6.65834817 1 25.81116667 371.9531709
131 12/15/2019 9:00 6.741466667 6.632475988 1 26.036 494.9472278
132 12/15/2019 10:00 6.802333333 6.616388921 1 26.31016667 581.4157
133 12/15/2019 11:00 6.872866667 6.600198303 1 26.34633333 630.5334859
134 12/15/2019 12:00 6.922933333 6.585644106 1 26.20933333 647.8361518
135 12/15/2019 13:00 6.939266667 6.582186542 1 26.50683333 631.9652932
136 12/15/2019 14:00 6.9002 6.578968315 1 26.65283333 574.7890604
137 12/15/2019 15:00 6.868266667 6.574499924 1 26.19416667 473.8616002
138 12/15/2019 16:00 6.8604 6.57583771 1 26.292 345.1493763
139 12/15/2019 17:00 6.8604 6.577350951 1 26.53516667 199.1131906
140 12/15/2019 18:00 6.876133333 6.575804822 1 26.41883333 74.12457176
141 12/15/2019 19:00 6.876733333 6.578377717 1 26.40016667 12.60987226
142 12/15/2019 20:00 6.837266667 6.584863685 1 26.37966667 0.308110425
143 12/15/2019 21:00 6.803533333 6.590561423 1 26.38616667 0
144 12/15/2019 22:00 6.735 6.597742565 1 26.342 0
145 12/15/2019 23:00 6.627866667 6.607310271 1 26.235 0
146 12/16/2019 0:00 6.487866667 6.618529915 1 26.1085 0
147 12/16/2019 1:00 6.3554 6.629848578 1 25.95733333 0
148 12/16/2019 2:00 6.251133333 6.641642103 1 25.80616667 0
149 12/16/2019 3:00 6.196066667 6.651515641 1 25.73016667 0.000453104
150 12/16/2019 4:00 6.1728 6.657394508 1 25.629 0.729949846
151 12/16/2019 5:00 6.1538 6.660707399 1 25.68933333 21.64521048
152 12/16/2019 6:00 6.149733333 6.655886692 1 25.7475 106.6438147
153 12/16/2019 7:00 6.166866667 6.630897122 1 25.82433333 237.6813662
154 12/16/2019 8:00 6.189866667 6.592497831 1 26.22 376.5172831
155 12/16/2019 9:00 6.263533333 6.553041981 1 27.08833333 497.8756361
156 12/16/2019 10:00 6.374466667 6.5231035 1 27.40383333 583.7287937
157 12/16/2019 11:00 6.4848 6.514413152 1 27.18066667 617.9485344
158 12/16/2019 12:00 6.6136 6.526676479 1 27.01133333 630.2901693
159 12/16/2019 13:00 6.696066667 6.54658944 1 26.78966667 617.3173611
160 12/16/2019 14:00 6.687733333 6.562516947 1 26.59283333 564.7247239
161 12/16/2019 15:00 6.653866667 6.574601807 1 26.4505 472.5988006
162 12/16/2019 16:00 6.5532 6.588082522 1 26.461 348.1081426
163 12/16/2019 17:00 6.433466667 6.602465872 1 26.39216667 214.8277285
164 12/16/2019 18:00 6.428466667 6.61409955 1 26.144 85.69275892
165 12/16/2019 19:00 6.428933333 6.625385647 1 26.085 14.66922797
166 12/16/2019 20:00 6.4754 6.631189523 1 26.17983333 0.222020748
167 12/16/2019 21:00 6.5448 6.631615083 1 26.21433333 0
168 12/16/2019 22:00 6.547066667 6.63316516 1 26.23183333 0
169 12/16/2019 23:00 6.527533333 6.635938818 1 26.17633333 0
170 12/17/2019 0:00 6.499333333 6.640191141 1 26.113 0
171 12/17/2019 1:00 6.431066667 6.646905986 1 26.08133333 0
172 12/17/2019 2:00 6.334666667 6.655913008 1 26.019 0
173 12/17/2019 3:00 6.219733333 6.666261918 1 25.87666667 0.003624829
174 12/17/2019 4:00 6.072066667 6.676497755 1 25.75916667 0.555958076
175 12/17/2019 5:00 6.037133333 6.676598284 1 25.722 14.97643218
176 12/17/2019 6:00 6.116733333 6.66027446 1 25.806 94.86991855
177 12/17/2019 7:00 6.195866667 6.631516354 1 26.28666667 233.0764746
178 12/17/2019 8:00 6.361666667 6.595683342 1 26.739 372.9259842
179 12/17/2019 9:00 6.508333333 6.569484454 1 27.01366667 494.9490402
180 12/17/2019 10:00 6.489466667 6.567230657 1 27.18983333 585.1977555
181 12/17/2019 11:00 6.461666667 6.575872502 1 26.709 630.3662907
182 12/17/2019 12:00 6.446533333 6.589070377 1 26.41466667 616.3875926
183 12/17/2019 13:00 6.444066667 6.597192932 1 26.48633333 589.063182
184 12/17/2019 14:00 6.5234 6.586262504 1 26.626 486.8398457
185 12/17/2019 15:00 6.652666667 6.570372601 1 26.62983333 445.8357853
186 12/17/2019 16:00 6.755066667 6.558340404 1 27.02083333 333.0361055
187 12/17/2019 17:00 6.773933333 6.552237098 1 26.97033333 192.5739999
188 12/17/2019 18:00 6.750533333 6.552780706 1 26.92633333 98.16715321
189 12/17/2019 19:00 6.702466667 6.558489849 1 26.88133333 23.15812329
190 12/17/2019 20:00 6.676666667 6.562883456 1 26.886 0.54372428
191 12/17/2019 21:00 6.687666667 6.565920926 1 26.88566667 0
192 12/17/2019 22:00 6.665733333 6.567346814 1 26.86216667 0
193 12/17/2019 23:00 6.592466667 6.570598057 1 26.864 0
194 12/18/2019 0:00 6.495666667 6.576159168 1 26.83916667 0
195 12/18/2019 1:00 6.363333333 6.584765074 1 26.71166667 0
196 12/18/2019 2:00 6.263466667 6.595698889 1 26.5315 0
197 12/18/2019 3:00 6.230733333 6.607048892 1 26.4005 0
stan model // b_Kn_oipi_tr_psrckm.stan which is attached b_Kn_oipi_tr_psrckm.stan (4.7 KB)
**Code to run the model**
dat<-data.frame(solar.time=as.POSIXct(Site$solar.time,tz="UTC",format="%Y-%m-%d %H:%M:%OS"),DO.obs=ma(Site$DO.obs,30),DO.sat=Site$DO.sat,depth=1,temp.water=Site$temp.water,light=Site$light)
sc6nm <- mm_name('bayes',GPP_fun='satlight',ER_fun='constant',pool_K600 ="normal", err_proc_acor = FALSE, err_proc_iid = TRUE)
sp6 <- specs(sc6nm,alpha_meanlog=.2,alpha_sdlog=.2,Pmax_mu=3,Pmax_sigma=.5,n_cores=4, n_chains=4, burnin_steps=2000, saved_steps=2000,day_start = -1.5,day_end = 23.5)
mm6 <- metab(sp6, data=dat)