First, we need to make sure that we are getting enough iterates in the fit:
controls <- list(maxit = 1000)We also clear out reps with not enough seeds (from 5/24/19), as well as dropping the reps that won’t converge on the generalized gamma (19, 40, and 77)
n_min <- 10 # Set the minimum number of dispersing seeds
dispersing_seeds <- group_by(disperseRIL, ID) %>%
filter(Distance > 4) %>%
filter(!(ID %in% c("19", "40", "77"))) %>%
summarize(tot_seeds=sum(Seedlings))
good_reps <- filter(dispersing_seeds, tot_seeds >= n_min) %>%
pull(ID)
good_reps [1] 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 20 21 22 23 24 25
[24] 26 27 28 29 31 33 34 35 36 37 39 41 42 43 44 45 46 48 53 54 55 56 57
[47] 58 59 60 62 66 68 70 73 74 75 78 79
80 Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 ... 80disperseRILgood <- filter(disperseRIL, ID %in% good_reps)So now fit all the reps.
RIL_list <- levels(disperseRILgood$RIL)
fiteach <- NULL
for (i in RIL_list) {
disperseRILi <- filter(disperseRILgood, RIL == i)
fiteachi <- cbind(RIL = i,
fiteach_disp_unt(disperseRILi,control=controls))
fiteach <- rbind(fiteach, fiteachi)
} <simpleError in optim(par = vstart, fn = fnobj, fix.arg = fix.arg, obs = data, gr = gradient, ddistnam = ddistname, hessian = TRUE, method = meth, lower = lower, upper = upper, ...): non-finite finite-difference value [1]>
Error in fitdist(cens_data_tble[, 2], model, start = start, ...) :
the function mle failed to estimate the parameters,
with the error code 100
<simpleError in optim(par = vstart, fn = fnobj, fix.arg = fix.arg, obs = data, gr = gradient, ddistnam = ddistname, hessian = TRUE, method = meth, lower = lower, upper = upper, ...): non-finite finite-difference value [1]>
Error in fitdist(cens_data_tble[, 2], model, start = start, ...) :
the function mle failed to estimate the parameters,
with the error code 100
<simpleError in optim(par = vstart, fn = fnobj, fix.arg = fix.arg, obs = data, gr = gradient, ddistnam = ddistname, hessian = TRUE, method = meth, lower = lower, upper = upper, ...): non-finite finite-difference value [2]>
Error in fitdist(cens_data_tble[, 2], model, start = start, ...) :
the function mle failed to estimate the parameters,
with the error code 100
<simpleError in optim(par = vstart, fn = fnobj, fix.arg = fix.arg, obs = data, gr = gradient, ddistnam = ddistname, hessian = TRUE, method = meth, lower = lower, upper = upper, ...): non-finite finite-difference value [2]>
Error in fitdist(cens_data_tble[, 2], model, start = start, ...) :
the function mle failed to estimate the parameters,
with the error code 100fiteach[, 1:7] RIL ID model AIC par1 par2 par3
1 3 2 hnorm 458.15374 5.0728328 NA NA
2 3 2 exp 471.10245 0.2427809 NA NA
3 3 2 lnorm 476.76897 1.1146174 0.86510626 NA
4 3 2 gamma 464.40835 1.5993266 0.38652505 NA
5 3 2 weibull 462.12028 1.3663451 4.50651400 NA
6 3 2 invgauss 479.64005 4.1560032 4.34513281 NA
7 3 2 logis 491.11799 3.8864002 1.68180344 NA
8 3 2 invgamma 495.32110 1.5524357 3.37984589 NA
9 3 2 gengamma 461.23963 1.7275301 0.61988153 1.68833369
10 3 3 hnorm 232.89988 3.1988298 NA NA
11 3 3 exp 239.73401 0.3897175 NA NA
12 3 3 lnorm 234.70727 0.7248461 0.71603983 NA
13 3 3 gamma 231.76494 2.0079107 0.77275820 NA
14 3 3 weibull 232.22391 1.4384875 2.85610856 NA
15 3 3 invgauss 235.55513 2.6140306 4.26046126 NA
16 3 3 logis 244.05186 2.4275784 0.93654292 NA
17 3 3 invgamma 241.30205 2.3334050 3.90186440 NA
18 3 3 gengamma 233.75953 0.9645710 0.70385477 0.73444698
19 3 4 hnorm 563.11863 5.9180967 NA NA
20 3 4 exp 565.55305 0.2200625 NA NA
21 3 4 lnorm 556.47545 1.1892868 0.84127958 NA
22 3 4 gamma 557.23577 1.5655014 0.34350608 NA
23 3 4 weibull 559.08008 1.2602841 4.91535706 NA
24 3 4 invgauss 555.90363 4.5670285 4.92108397 NA
25 3 4 logis 611.16610 3.9934580 1.99349823 NA
26 3 4 invgamma 565.91473 1.7156121 4.14359814 NA
27 3 4 gengamma 557.43082 1.3303133 0.83808846 0.35061590
28 3 5 hnorm 194.87525 5.0770862 NA NA
29 3 5 exp 190.92349 0.2722972 NA NA
30 3 5 lnorm 191.99124 0.9420168 0.89094703 NA
31 3 5 gamma 191.55861 1.3249885 0.35954668 NA
32 3 5 weibull 191.96416 1.1371575 3.86223638 NA
33 3 5 invgauss 192.66144 3.7088418 3.51351925 NA
34 3 5 logis 211.54128 3.1824674 1.61656948 NA
35 3 5 invgamma 196.44921 1.6215041 3.04109145 NA
36 3 5 gengamma 193.07350 1.1545130 0.89456207 0.52020188
37 3 6 hnorm 39.33646 2.6255386 NA NA
38 3 6 exp 42.32422 0.4382552 NA NA
39 3 6 lnorm 41.79378 0.6797445 0.61838545 NA
40 3 6 gamma 40.63440 2.8772475 1.23788567 NA
41 3 6 weibull 39.89722 1.9524018 2.61343547 NA
42 3 6 invgauss 41.82581 2.3325521 5.41911910 NA
43 3 6 logis 41.29484 2.3073806 0.74219665 NA
44 3 6 invgamma 43.16830 2.8914938 4.80260396 NA
45 3 6 gengamma 40.32503 1.4252451 0.10487829 8.48019289
46 18 7 hnorm 614.43192 8.4609242 NA NA
47 18 7 exp 621.53209 0.1504588 NA NA
48 18 7 lnorm 628.53629 1.5401276 0.93168525 NA
49 18 7 gamma 616.69138 1.4439631 0.21694666 NA
50 18 7 weibull 615.87905 1.2605985 7.15329463 NA
51 18 7 invgauss 634.45505 6.6696869 5.50894619 NA
52 18 7 logis 658.11968 6.0290592 2.86632528 NA
53 18 7 invgamma 653.16326 1.2983192 3.98597064 NA
54 18 7 gengamma 617.67072 2.0246366 0.76998463 1.14629111
55 18 8 hnorm 646.12910 6.3578818 NA NA
56 18 8 exp 660.08596 0.1957837 NA NA
57 18 8 lnorm 659.54403 1.3329190 0.84413606 NA
58 18 8 gamma 647.66459 1.6732138 0.32662500 NA
59 18 8 weibull 646.67071 1.3639613 5.59244383 NA
60 18 8 invgauss 664.43652 5.1352833 5.50255411 NA
61 18 8 logis 688.30926 4.6704410 2.07745827 NA
62 18 8 invgamma 683.98014 1.5741422 4.26189558 NA
63 18 8 gengamma 648.61623 1.7468992 0.72348240 1.07006592
64 18 9 hnorm 886.77246 6.2356568 NA NA
65 18 9 exp 903.68457 0.2010221 NA NA
66 18 9 lnorm 915.72600 1.2681787 0.91118852 NA
67 18 9 gamma 894.62087 1.4665865 0.29396355 NA
68 18 9 weibull 891.88242 1.2899895 5.38076345 NA
69 18 9 invgauss 922.39903 5.0073388 4.54962020 NA
70 18 9 logis 955.15659 4.6151571 2.13943612 NA
71 18 9 invgamma 950.93415 1.4086476 3.43717896 NA
72 18 9 gengamma 890.57757 1.8787874 0.67925445 1.55400030
73 18 10 hnorm 146.33282 3.0654828 NA NA
74 18 10 exp 153.33945 0.3930432 NA NA
75 18 10 lnorm 155.06971 0.7002472 0.77081944 NA
76 18 10 gamma 150.50325 1.8580601 0.72101422 NA
77 18 10 weibull 148.97677 1.5079404 2.84343908 NA
78 18 10 invgauss 155.31031 2.5974444 3.70694073 NA
79 18 10 logis 158.09461 2.4944856 0.99103886 NA
80 18 10 invgamma 160.52474 2.0272986 3.20487824 NA
81 18 10 gengamma 147.00661 1.4436439 0.41475236 2.78474104
82 22 11 hnorm 1059.23344 5.7150700 NA NA
83 22 11 exp 1064.75135 0.2274300 NA NA
84 22 11 lnorm 1092.30639 1.0798343 1.00461234 NA
85 22 11 gamma 1064.01024 1.1899227 0.27005804 NA
86 22 11 weibull 1062.08666 1.1433079 4.61129324 NA
87 22 11 invgauss 1100.12562 4.4355744 3.25675964 NA
88 22 11 logis 1158.28527 4.0060255 2.00400537 NA
89 22 11 invgamma 1134.60174 1.2591476 2.45057640 NA
90 22 11 gengamma 1058.27990 1.7686313 0.76554892 1.62830185
91 22 12 hnorm 523.68660 5.7961324 NA NA
92 22 12 exp 547.00579 0.2032048 NA NA
93 22 12 lnorm 553.38123 1.3289967 0.83540320 NA
94 22 12 gamma 533.03898 1.8459909 0.37362268 NA
95 22 12 weibull 526.44151 1.5657110 5.46372611 NA
96 22 12 invgauss 559.79607 4.9542987 5.53735206 NA
97 22 12 logis 545.11605 4.8426415 1.83658763 NA
98 22 12 invgamma 581.45544 1.5161531 4.03210507 NA
99 22 12 gengamma 507.23272 2.1641151 0.27397943 3.92266313
100 22 13 hnorm 829.06873 6.2078198 NA NA
101 22 13 exp 845.70998 0.2014226 NA NA
102 22 13 lnorm 848.99733 1.2852737 0.87423637 NA
103 22 13 gamma 833.15655 1.5709738 0.31545937 NA
104 22 13 weibull 831.39060 1.3263288 5.40568600 NA
105 22 13 invgauss 853.77929 4.9942432 4.97277119 NA
106 22 13 logis 889.60456 4.5749979 2.09121055 NA
107 22 13 invgamma 878.72302 1.5074418 3.83193607 NA
108 22 13 gengamma 832.65741 1.7803208 0.71354476 1.25405677
109 22 14 hnorm 720.32032 6.9156276 NA NA
110 22 14 exp 750.91325 0.1698973 NA NA
111 22 14 lnorm 726.88503 1.5490114 0.73069832 NA
112 22 14 gamma 713.16533 2.2922453 0.38856662 NA
113 22 14 weibull 710.02451 1.6711135 6.60500860 NA
114 22 14 invgauss 730.60985 5.9051663 8.81949334 NA
115 22 14 logis 739.02046 5.6573319 2.09489648 NA
116 22 14 invgamma 752.63438 1.9280730 6.88725268 NA
117 22 14 gengamma 711.51118 1.9524634 0.56711788 1.21571122
118 22 15 hnorm 142.55087 3.0621983 NA NA
119 22 15 exp 146.30988 0.4098996 NA NA
120 22 15 lnorm 147.53286 0.6169957 0.80681935 NA
121 22 15 gamma 145.44252 1.6008811 0.64905614 NA
122 22 15 weibull 145.05873 1.3277812 2.67584346 NA
123 22 15 invgauss 147.12373 2.4879878 3.17689632 NA
124 22 15 logis 159.61755 2.2778274 1.05431627 NA
125 22 15 invgamma 150.48626 2.0007747 2.91202366 NA
126 22 15 gengamma 143.72799 1.8040929 0.08598207 16.70716803
127 22 16 hnorm 437.90961 5.9194830 NA NA
128 22 16 exp 439.56730 0.2203067 NA NA
129 22 16 lnorm 446.03575 1.1453999 0.93741284 NA
130 22 16 gamma 438.51756 1.3277279 0.29166382 NA
131 22 16 weibull 438.16714 1.1893746 4.82158135 NA
132 22 16 invgauss 448.44544 4.5722701 3.88363772 NA
133 22 16 logis 476.82110 4.0677025 2.02029921 NA
134 22 16 invgamma 460.82800 1.4029369 3.03677316 NA
135 22 16 gengamma 440.07215 1.6203417 0.82459846 1.11697516
136 35 17 hnorm 187.68268 6.8615549 NA NA
137 35 17 exp 187.49058 0.1923722 NA NA
138 35 17 lnorm 195.56030 1.1058946 1.20625870 NA
139 35 17 gamma 189.27469 0.8894555 0.17130199 NA
140 35 17 weibull 189.47617 0.9813564 5.15900723 NA
141 35 17 invgauss 197.18922 5.2342980 2.48236916 NA
142 35 17 logis 210.40290 4.7750007 2.64432150 NA
143 35 17 invgamma 203.23509 0.9601631 1.67373092 NA
144 35 17 gengamma 182.10366 2.6624522 0.10475943 17.77130677
145 35 18 hnorm 125.57793 4.7628874 NA NA
146 35 18 exp 129.44710 0.2573362 NA NA
147 35 18 lnorm 129.20095 1.0624546 0.82626164 NA
148 35 18 gamma 127.89305 1.7262484 0.44222663 NA
149 35 18 weibull 127.58453 1.4114109 4.28884139 NA
150 35 18 invgauss 128.36804 3.9093909 4.55417833 NA
151 35 18 logis 137.40794 3.7370034 1.65584290 NA
152 35 18 invgamma 131.33866 1.7424410 3.71492989 NA
153 35 18 gengamma 127.52557 2.0843603 0.25346085 4.83019215
154 35 20 hnorm 207.77929 5.0075700 NA NA
155 35 20 exp 212.26485 0.2498801 NA NA
156 35 20 lnorm 211.50450 1.1011402 0.81337831 NA
157 35 20 gamma 208.96391 1.7112172 0.42560996 NA
158 35 20 weibull 208.93567 1.3623853 4.39177945 NA
159 35 20 invgauss 212.03205 4.0325187 4.80713974 NA
160 35 20 logis 224.27279 3.6547286 1.63651921 NA
161 35 20 invgamma 217.35252 1.7746021 3.97952262 NA
162 35 20 gengamma 210.90201 1.4425759 0.74598325 0.89833253
163 35 21 hnorm 469.57166 4.3822941 NA NA
164 35 21 exp 477.70632 0.2892642 NA NA
165 35 21 lnorm 462.01071 0.9800354 0.75240540 NA
166 35 21 gamma 462.73946 1.8684227 0.53720110 NA
167 35 21 weibull 465.34235 1.3746111 3.81385860 NA
168 35 21 invgauss 461.90061 3.4865036 4.95360656 NA
169 35 21 logis 502.14670 3.1100821 1.37930104 NA
170 35 21 invgamma 469.52497 2.1173073 4.42237669 NA
171 35 21 gengamma 463.16417 1.0925005 0.75471775 0.31568665
172 35 22 hnorm 161.34414 3.9280437 NA NA
173 35 22 exp 176.87368 0.2731136 NA NA
174 35 22 lnorm 145.05140 1.2226877 0.43211114 NA
175 35 22 gamma 140.73560 6.1368882 1.66511656 NA
176 35 22 weibull 136.87498 3.0031810 4.12778468 NA
177 35 22 invgauss 146.10663 3.6845982 17.91657580 NA
178 35 22 logis 139.03394 3.6918626 0.80072405 NA
179 35 22 invgamma 151.44962 5.0143221 15.37407813 NA
180 35 22 gengamma 137.78185 1.5265770 0.26806873 1.72806284
181 42 23 hnorm 562.27710 5.6421080 NA NA
182 42 23 exp 569.31306 0.2262570 NA NA
183 42 23 lnorm 575.61600 1.1659351 0.88092518 NA
184 42 23 gamma 563.55734 1.4992799 0.33800140 NA
185 42 23 weibull 562.76349 1.2749574 4.77544905 NA
186 42 23 invgauss 580.91194 4.4557272 4.37489731 NA
187 42 23 logis 601.56434 3.9827461 1.80499903 NA
188 42 23 invgamma 598.69477 1.5077385 3.42311212 NA
189 42 23 gengamma 564.69066 1.5923297 0.77565717 1.07748623
190 42 24 hnorm 55.68608 3.8044885 NA NA
191 42 24 exp 58.69634 0.3083005 NA NA
192 42 24 lnorm 60.34459 0.9452909 0.77202636 NA
193 42 24 gamma 58.38754 2.0146095 0.61575777 NA
194 42 24 weibull 57.54039 1.6455320 3.63944546 NA
195 42 24 invgauss 60.53028 3.2852255 4.59338987 NA
196 42 24 logis 59.82271 3.2729132 1.19802104 NA
197 42 24 invgamma 62.67331 1.8761553 3.66902028 NA
198 42 24 gengamma 56.04587 1.8185937 0.12479103 8.23285292
199 42 25 hnorm 179.98898 7.1721229 NA NA
200 42 25 exp 184.31585 0.1718507 NA NA
201 42 25 lnorm 194.17292 1.3274088 1.10845156 NA
202 42 25 gamma 186.10083 1.1292066 0.19383098 NA
203 42 25 weibull 185.32866 1.1820052 6.12907939 NA
204 42 25 invgauss 196.86454 5.8563158 3.37774733 NA
205 42 25 logis 195.23614 5.7776249 2.55534354 NA
206 42 25 invgamma 203.83117 0.9963970 2.18071973 NA
207 42 25 gengamma 177.97745 2.3535731 0.39723391 3.56693360
208 42 26 hnorm 325.31489 3.9391971 NA NA
209 42 26 exp 335.18556 0.3136573 NA NA
210 42 26 lnorm 334.30507 0.8963065 0.79310374 NA
211 42 26 gamma 327.98251 1.7607238 0.54797223 NA
212 42 26 weibull 327.01168 1.4032969 3.51959560 NA
213 42 26 invgauss 335.26598 3.2298307 4.18603552 NA
214 42 26 logis 349.73528 2.9791707 1.27079384 NA
215 42 26 invgamma 344.77255 1.8983144 3.56266106 NA
216 42 26 gengamma 328.71883 1.3376319 0.68304815 1.23649537
217 42 27 hnorm 385.69359 3.9740326 NA NA
218 42 27 exp 404.93750 0.2981240 NA NA
219 42 27 lnorm 394.09557 1.0016856 0.71293646 NA
220 42 27 gamma 384.80071 2.2540643 0.66651785 NA
221 42 27 weibull 382.34387 1.6361360 3.76991555 NA
222 42 27 invgauss 395.82365 3.3909273 5.55951452 NA
223 42 27 logis 398.16769 3.2349247 1.17672627 NA
224 42 27 invgamma 408.63790 2.1565240 4.62378854 NA
225 42 27 gengamma 383.82205 1.3981722 0.58272164 1.24497556
226 42 28 hnorm 110.79583 3.1449788 NA NA
227 42 28 exp 113.55870 0.3997997 NA NA
228 42 28 lnorm 112.75845 0.6788591 0.74183477 NA
229 42 28 gamma 111.85862 1.8426531 0.72751223 NA
230 42 28 weibull 112.01241 1.3841172 2.76827128 NA
231 42 28 invgauss 112.85257 2.5492181 3.85616781 NA
232 42 28 logis 120.69318 2.3007351 0.97952734 NA
233 42 28 invgamma 115.08937 2.2724593 3.61521582 NA
234 42 28 gengamma 113.85786 0.9219415 0.73807947 0.71758010
235 53 29 hnorm 67.55424 3.3150913 NA NA
236 53 29 exp 74.18867 0.3266835 NA NA
237 53 29 lnorm 59.09316 1.0476989 0.41133834 NA
238 53 29 gamma 58.68563 6.2210268 2.01412702 NA
239 53 29 weibull 58.65240 2.8023825 3.47708686 NA
240 53 29 invgauss 58.94490 3.0910776 17.07500496 NA
241 53 29 logis 60.83925 3.0462407 0.72275704 NA
242 53 29 invgamma 59.82556 6.2517955 16.47874995 NA
243 53 29 gengamma 60.59255 1.1909755 0.37989830 0.71571696
244 53 31 hnorm 136.54671 5.3407727 NA NA
245 53 31 exp 141.21288 0.2267743 NA NA
246 53 31 lnorm 123.61831 1.3212789 0.54157067 NA
247 53 31 gamma 128.44636 3.1465402 0.71106293 NA
248 53 31 weibull 132.80563 1.6494639 4.99854001 NA
249 53 31 invgauss 123.30826 4.4241641 12.95369519 NA
250 53 31 logis 139.52560 3.8354740 1.41165619 NA
251 53 31 invgamma 120.92466 4.1882659 13.90421375 NA
252 53 31 gengamma 121.53493 1.0526618 0.38493929 -1.18361954
253 53 33 hnorm 55.77764 2.5818713 NA NA
254 53 33 exp 62.28383 0.4161611 NA NA
255 53 33 lnorm 44.17066 0.8330661 0.34469373 NA
256 53 33 gamma 44.38058 8.3913392 3.44149690 NA
257 53 33 weibull 45.52245 3.0380415 2.72905872 NA
258 53 33 invgauss 44.07025 2.4406079 19.44500650 NA
259 53 33 logis 46.52242 2.3793905 0.48975069 NA
260 53 33 invgamma 44.23183 9.1574527 20.00396682 NA
261 53 33 gengamma 46.16282 0.8197345 0.34250222 -0.08215672
262 53 34 hnorm 163.87343 3.6491893 NA NA
263 53 34 exp 169.51548 0.3364732 NA NA
264 53 34 lnorm 169.21773 0.8393598 0.77230135 NA
265 53 34 gamma 166.18745 1.8319547 0.61091517 NA
266 53 34 weibull 165.64056 1.4359365 3.29539694 NA
267 53 34 invgauss 169.51497 3.0146317 4.17811554 NA
268 53 34 logis 177.35840 2.7839259 1.17774113 NA
269 53 34 invgamma 174.11866 2.0111251 3.62635071 NA
270 53 34 gengamma 167.41309 1.2997782 0.65351423 1.32783093
271 58 35 hnorm 88.91368 3.1884913 NA NA
272 58 35 exp 93.72269 0.3722395 NA NA
273 58 35 lnorm 89.90022 0.8065209 0.65127224 NA
274 58 35 gamma 88.96684 2.5047055 0.92122290 NA
275 58 35 weibull 88.92285 1.6756736 3.04257332 NA
276 58 35 invgauss 89.89725 2.7253363 5.52722864 NA
277 58 35 logis 94.05552 2.5437595 0.95003207 NA
278 58 35 invgamma 91.83588 2.7041599 5.02374632 NA
279 58 35 gengamma 90.89634 1.0698718 0.61029292 0.85689556
280 58 36 hnorm 128.21552 6.0337941 NA NA
281 58 36 exp 131.78263 0.2031263 NA NA
282 58 36 lnorm 119.65764 1.3979588 0.60147105 NA
283 58 36 gamma 123.53862 2.6629482 0.53958574 NA
284 58 36 weibull 126.29712 1.5728152 5.55419704 NA
285 58 36 invgauss 118.82117 4.9338950 11.57513694 NA
286 58 36 logis 135.28617 4.2783099 1.78811634 NA
287 58 36 invgamma 117.26593 3.4040634 11.82819016 NA
288 58 36 gengamma 116.20471 0.7988170 0.19461464 -3.63870677
289 58 37 hnorm 165.26090 4.1369138 NA NA
290 58 37 exp 170.61260 0.2967330 NA NA
291 58 37 lnorm 163.38822 0.9898403 0.70195045 NA
292 58 37 gamma 163.41951 2.1743032 0.64090800 NA
293 58 37 weibull 164.43410 1.5041410 3.76929464 NA
294 58 37 invgauss 163.15604 3.3975474 5.68592304 NA
295 58 37 logis 175.36948 3.1050712 1.26922378 NA
296 58 37 invgamma 165.90885 2.3505670 5.07383272 NA
297 58 37 gengamma 165.04642 1.1036646 0.69947353 0.33759010
298 58 39 hnorm 52.37337 3.9369763 NA NA
299 58 39 exp 55.40175 0.2947989 NA NA
300 58 39 lnorm 57.22091 1.0063071 0.75576733 NA
301 58 39 gamma 55.03219 2.1258288 0.62115739 NA
302 58 39 weibull 54.03948 1.7211370 3.81350250 NA
303 58 39 invgauss 57.68033 3.4365235 5.02945037 NA
304 58 39 logis 55.56545 3.4131476 1.19539139 NA
305 58 39 invgamma 59.92632 1.8935695 3.95139339 NA
306 58 39 gengamma 52.29462 1.8353291 0.09989949 9.71093066
307 101 41 hnorm 220.66858 6.5301479 NA NA
308 101 41 exp 228.35037 0.1839218 NA NA
309 101 41 lnorm 226.76610 1.4408375 0.78229470 NA
310 101 41 gamma 221.94673 1.9874256 0.36437872 NA
311 101 41 weibull 221.08338 1.5290502 6.04636165 NA
312 101 41 invgauss 228.58269 5.4612624 6.99469525 NA
313 101 41 logis 230.94494 5.1859395 2.04653176 NA
314 101 41 invgamma 235.66057 1.7330206 5.38579617 NA
315 101 41 gengamma 222.94554 1.8561720 0.62986035 1.17738398
316 101 42 hnorm 116.08575 5.2041615 NA NA
317 101 42 exp 119.34092 0.2363889 NA NA
318 101 42 lnorm 119.45837 1.1594615 0.81198623 NA
319 101 42 gamma 117.91562 1.7768804 0.41827266 NA
320 101 42 weibull 117.73064 1.4163519 4.66808314 NA
321 101 42 invgauss 119.41851 4.2563694 5.10308615 NA
322 101 42 logis 125.59661 3.9849228 1.72734686 NA
323 101 42 invgamma 122.45431 1.7500598 4.12712702 NA
324 101 42 gengamma 119.70304 1.5918147 0.68365399 1.14414832
325 101 43 hnorm 45.21672 2.9154080 NA NA
326 101 43 exp 49.39777 0.3794904 NA NA
327 101 43 lnorm 43.60232 0.8775361 0.47987092 NA
328 101 43 gamma 42.65031 4.7353405 1.77407657 NA
329 101 43 weibull 42.35583 2.3892793 3.00537586 NA
330 101 43 invgauss 43.83839 2.6681994 10.44969641 NA
331 101 43 logis 42.33053 2.6161161 0.64112213 NA
332 101 43 invgamma 45.16303 4.3690720 9.34744920 NA
333 101 43 gengamma 44.33462 1.0768783 0.42525571 0.88675398
334 101 44 hnorm 165.12306 4.6547441 NA NA
335 101 44 exp 171.58553 0.2585742 NA NA
336 101 44 lnorm 164.61046 1.1344544 0.69983711 NA
337 101 44 gamma 163.53724 2.2850741 0.58776525 NA
338 101 44 weibull 164.04264 1.5814986 4.34070073 NA
339 101 44 invgauss 164.53990 3.8920264 6.54608555 NA
340 101 44 logis 173.09409 3.6411532 1.41562038 NA
341 101 44 invgamma 168.13786 2.2687291 5.60274595 NA
342 101 44 gengamma 165.52458 1.3364200 0.66793891 0.59907742
343 101 45 hnorm 85.26188 3.5016903 NA NA
344 101 45 exp 89.60779 0.3392158 NA NA
345 101 45 lnorm 84.68787 0.9064401 0.62831326 NA
346 101 45 gamma 84.25846 2.6767664 0.89919320 NA
347 101 45 weibull 84.75998 1.6845978 3.33696216 NA
348 101 45 invgauss 84.80234 2.9815158 6.44991488 NA
349 101 45 logis 88.61441 2.7732487 0.99090880 NA
350 101 45 invgamma 86.42324 2.8371697 5.86541928 NA
351 101 45 gengamma 86.22737 1.0534954 0.61873821 0.48930908
352 101 46 hnorm 204.59039 4.1663099 NA NA
353 101 46 exp 213.43801 0.2876821 NA NA
354 101 46 lnorm 197.57609 1.0521563 0.64175684 NA
355 101 46 gamma 198.77317 2.5657298 0.73347833 NA
356 101 46 weibull 200.79793 1.6372391 3.92609343 NA
357 101 46 invgauss 196.95217 3.4991265 7.17296472 NA
358 101 46 logis 213.92109 3.2114829 1.25145621 NA
359 101 46 invgamma 199.27385 2.7686492 6.57525544 NA
360 101 46 gengamma 199.56133 1.0719012 0.64287200 0.06280545
361 133 48 hnorm 227.39419 3.7444630 NA NA
362 133 48 exp 240.43685 0.3123745 NA NA
363 133 48 lnorm 238.31226 0.9508513 0.73697990 NA
364 133 48 gamma 230.51740 2.1818207 0.67528896 NA
365 133 48 weibull 227.18006 1.6919449 3.60414704 NA
366 133 48 invgauss 239.31365 3.2423931 5.00893102 NA
367 133 48 logis 235.63735 3.1896442 1.13177594 NA
368 133 48 invgamma 248.18755 2.0203038 4.05467646 NA
369 133 48 gengamma 223.47735 1.5966923 0.38793422 2.48406395
370 144 53 hnorm 196.77086 6.2709292 NA NA
371 144 53 exp 205.61041 0.1868157 NA NA
372 144 53 lnorm 190.25189 1.5113154 0.60160378 NA
373 144 53 gamma 189.47014 3.0186563 0.56227411 NA
374 144 53 weibull 191.59053 1.7601723 6.04879164 NA
375 144 53 invgauss 191.58472 5.3699739 12.34870402 NA
376 144 53 logis 197.04195 4.9569895 1.66950909 NA
377 144 53 invgamma 195.55888 2.8332112 10.68406320 NA
378 144 53 gengamma 191.23981 1.6258436 0.58723596 0.39193583
379 144 54 hnorm 235.72009 5.8087208 NA NA
380 144 54 exp 238.07748 0.2210370 NA NA
381 144 54 lnorm 232.98268 1.2375318 0.76918302 NA
382 144 54 gamma 232.78032 1.8248788 0.40187482 NA
383 144 54 weibull 234.17122 1.3458767 4.96549699 NA
384 144 54 invgauss 234.30567 4.5510050 5.98140105 NA
385 144 54 logis 249.89960 3.9840993 1.76218500 NA
386 144 54 invgamma 238.94770 1.9382319 5.10427729 NA
387 144 54 gengamma 234.07557 1.3841810 0.76324654 0.40028808
388 144 55 hnorm 73.95012 2.9097058 NA NA
389 144 55 exp 75.87063 0.4321341 NA NA
390 144 55 lnorm 81.51324 0.4520047 1.02091907 NA
391 144 55 gamma 77.85200 1.0598026 0.45694202 NA
392 144 55 weibull 77.57237 1.1467090 2.43394330 NA
393 144 55 invgauss 81.79908 2.3718810 1.87196821 NA
394 144 55 logis 85.03256 2.2945424 1.05924941 NA
395 144 55 invgamma 85.05366 1.3626372 1.52900591 NA
396 144 55 gengamma 72.14078 1.6471677 0.12660133 12.74371598
397 144 56 hnorm 181.07490 6.2423292 NA NA
398 144 56 exp 187.49058 0.1923722 NA NA
399 144 56 lnorm 177.04237 1.4488385 0.65609460 NA
400 144 56 gamma 176.86083 2.5447843 0.48807116 NA
401 144 56 weibull 178.49078 1.6192843 5.84577976 NA
402 144 56 invgauss 177.72607 5.2172820 9.92301958 NA
403 144 56 logis 186.42335 4.7609665 1.79202219 NA
404 144 56 invgamma 181.03263 2.4880402 8.58765126 NA
405 144 56 gengamma 178.46781 1.5597106 0.64588347 0.34664482
406 144 57 hnorm 174.73694 4.9869302 NA NA
407 144 57 exp 173.99079 0.2668045 NA NA
408 144 57 lnorm 174.30822 0.9668857 0.88403509 NA
409 144 57 gamma 174.25488 1.3865917 0.36862409 NA
410 144 57 weibull 174.57625 1.1820105 3.98668192 NA
411 144 57 invgauss 173.93645 3.7783165 3.68308610 NA
412 144 57 logis 193.24083 3.2804523 1.69493696 NA
413 144 57 invgamma 177.03613 1.6462465 3.16254617 NA
414 144 57 gengamma 175.87357 1.1521430 0.88471275 0.44785154
415 144 58 hnorm 334.43671 4.7081753 NA NA
416 144 58 exp 329.24841 0.2899832 NA NA
417 144 58 lnorm 328.16313 0.8713335 0.89379658 NA
418 144 58 gamma 328.95496 1.3108486 0.37872206 NA
419 144 58 weibull 329.61252 1.1357858 3.62604792 NA
420 144 58 invgauss 327.53172 3.4820931 3.31406620 NA
421 144 58 logis 368.78867 2.9961129 1.59220982 NA
422 144 58 invgamma 332.71225 1.6671345 2.93799649 NA
423 144 58 gengamma 329.66084 1.0136538 0.90517349 0.34730944
424 147 59 hnorm 209.37559 4.8384997 NA NA
425 147 59 exp 214.75429 0.2563527 NA NA
426 147 59 lnorm 219.80817 1.0561647 0.87606921 NA
427 147 59 gamma 213.52448 1.5367851 0.39203525 NA
428 147 59 weibull 212.47650 1.3343983 4.25015855 NA
429 147 59 invgauss 221.63351 3.9423906 4.03368881 NA
430 147 59 logis 225.84725 3.6418708 1.58714372 NA
431 147 59 invgamma 229.10772 1.5355771 3.15675191 NA
432 147 59 gengamma 213.19200 1.6529615 0.65452586 1.62829576
433 147 60 hnorm 291.20399 5.8481763 NA NA
434 147 60 exp 300.83118 0.2071433 NA NA
435 147 60 lnorm 287.32836 1.3627953 0.68678832 NA
436 147 60 gamma 285.35426 2.3570512 0.48637947 NA
437 147 60 weibull 287.21597 1.5655873 5.40776169 NA
438 147 60 invgauss 289.34678 4.8507527 8.28116460 NA
439 147 60 logis 299.19221 4.3999661 1.65534461 NA
440 147 60 invgamma 296.21606 2.2509855 6.96959670 NA
441 147 60 gengamma 287.16919 1.5297404 0.66326967 0.50771265
442 147 62 hnorm 146.44175 4.6142883 NA NA
443 147 62 exp 151.46583 0.2638143 NA NA
444 147 62 lnorm 148.29864 1.1003849 0.73150934 NA
445 147 62 gamma 146.51102 2.0935250 0.54904098 NA
446 147 62 weibull 146.65841 1.5113427 4.22886075 NA
447 147 62 invgauss 148.81528 3.8202364 5.80771291 NA
448 147 62 logis 154.45658 3.5241588 1.39515947 NA
449 147 62 invgamma 152.60923 2.0889920 4.89650937 NA
450 147 62 gengamma 148.48916 1.3663895 0.68192370 0.77192213
451 148 66 hnorm 89.69667 5.5226749 NA NA
452 148 66 exp 91.62335 0.2259566 NA NA
453 148 66 lnorm 94.15612 1.1375840 0.91921517 NA
454 148 66 gamma 92.54872 1.4395743 0.32425875 NA
455 148 66 weibull 92.27393 1.2833823 4.78471325 NA
456 148 66 invgauss 94.00512 4.4537245 4.02950370 NA
457 148 66 logis 99.53026 4.2094188 1.98656897 NA
458 148 66 invgamma 96.50408 1.4463222 3.12345286 NA
459 148 66 gengamma 90.59293 2.3475411 0.09499092 14.12584780
460 148 68 hnorm 84.23829 4.7434087 NA NA
461 148 68 exp 85.74323 0.2662692 NA NA
462 148 68 lnorm 88.81901 0.9581814 0.94157509 NA
463 148 68 gamma 87.12965 1.3284015 0.35239219 NA
464 148 68 weibull 86.88885 1.2239486 4.01817741 NA
465 148 68 invgauss 88.67705 3.7895545 3.30690434 NA
466 148 68 logis 94.75434 3.5614008 1.74060015 NA
467 148 68 invgamma 91.04908 1.4473678 2.63621412 NA
468 148 68 gengamma 85.91254 2.2457009 0.10768868 13.82049447
469 148 70 hnorm 59.51212 5.3072291 NA NA
470 148 70 exp 60.67046 0.2363889 NA NA
471 148 70 lnorm 61.61846 1.1496332 0.81750901 NA
472 148 70 gamma 61.13058 1.7179689 0.40454496 NA
473 148 70 weibull 61.18051 1.3608931 4.64244581 NA
474 148 70 invgauss 61.58273 4.2561058 4.98719092 NA
475 148 70 logis 65.31200 3.9153315 1.72610471 NA
476 148 70 invgamma 62.94985 1.7530253 4.09407491 NA
477 148 70 gengamma 63.13058 1.4463690 0.76282858 0.76363845
478 180 73 hnorm 226.26420 6.1815928 NA NA
479 180 73 exp 233.07428 0.1970625 NA NA
480 180 73 lnorm 239.00707 1.3200393 0.89008194 NA
481 180 73 gamma 231.10447 1.5948681 0.31329577 NA
482 180 73 weibull 229.54893 1.3910907 5.55157545 NA
483 180 73 invgauss 242.07582 5.1106313 4.89991564 NA
484 180 73 logis 240.40963 4.8144995 2.00741840 NA
485 180 73 invgamma 250.81800 1.3915976 3.55673338 NA
486 180 73 gengamma 229.53447 1.9373715 0.60333352 1.72521596
487 180 74 hnorm 67.08023 2.6670926 NA NA
488 180 74 exp 75.36490 0.3968822 NA NA
489 180 74 lnorm 51.59331 0.8919704 0.31565123 NA
490 180 74 gamma 50.94366 10.3224403 4.03949933 NA
491 180 74 weibull 49.96426 3.7984177 2.83216466 NA
492 180 74 invgauss 51.49734 2.5590636 24.69955443 NA
493 180 74 logis 52.25574 2.5627728 0.46645957 NA
494 180 74 invgamma 52.39018 10.5407540 24.60132844 NA
495 180 74 gengamma 50.90042 1.2139391 0.13009084 3.18322164
496 180 75 hnorm 64.32957 2.7181336 NA NA
497 180 75 exp 72.32946 0.3877664 NA NA
498 180 75 lnorm 48.77650 0.9185454 0.30202874 NA
499 180 75 gamma 48.05731 11.2555005 4.30629097 NA
500 180 75 weibull 46.77151 4.0312105 2.88694884 NA
501 180 75 invgauss 48.70829 2.6173574 27.70913498 NA
502 180 75 logis 48.87447 2.6316858 0.45293133 NA
503 180 75 invgamma 49.60928 11.4431865 27.52048668 NA
504 180 75 gengamma 47.54043 1.2190512 0.12342166 3.14724615
505 187 78 hnorm 370.76358 6.4892543 NA NA
506 187 78 exp 373.70057 0.1986994 NA NA
507 187 78 lnorm 360.86510 1.3350485 0.76763848 NA
508 187 78 gamma 363.66184 1.8371081 0.36411444 NA
509 187 78 weibull 366.52030 1.3436159 5.52844786 NA
510 187 78 invgauss 360.81950 5.0510790 6.64855384 NA
511 187 78 logis 394.17607 4.4418527 2.04768847 NA
512 187 78 invgamma 365.98222 1.9768520 5.75172157 NA
513 187 78 gengamma 362.73904 1.3834386 0.76882649 0.13019975
514 187 79 hnorm 124.75266 5.6291044 NA NA
515 187 79 exp 122.91270 0.2427306 NA NA
516 187 79 lnorm 126.80724 0.9772159 1.02378992 NA
517 187 79 gamma 124.83202 1.0901925 0.26434385 NA
518 187 79 weibull 124.80303 1.0595625 4.21599693 NA
519 187 79 invgauss 127.21837 4.1551139 2.88741478 NA
520 187 79 logis 138.68394 3.6374276 1.95768049 NA
521 187 79 invgamma 130.48762 1.2794451 2.27504581 NA
522 187 79 gengamma 126.76050 1.5067835 0.92242454 1.15401997Now lets calculate the delta-AIC within each dataset:
result <- group_by(fiteach, ID) %>% mutate(delta_AIC = AIC - min(AIC))
ggplot(result, aes(x=delta_AIC, group = model)) + geom_histogram() +
facet_wrap(~model, scales = "free") `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Once again, we confirm that the generalized gamma is the only model that always has a low \(\Delta\)-AIC.
Let’s look at the fitted kernels:
fiteachgg <- filter(fiteach, model == "gengamma")
p <- ggplot(data = data.frame(x = c(0, 20)), mapping = aes(x = x))
for (i in 1:nrow(fiteachgg)) {
pvec <- as.numeric(fiteachgg[i, 5:7])
plist <- list(mu = pvec[1], sigma = pvec[2], Q= pvec[3])
p <- p + stat_function(fun = dgengamma, args = plist, color = fiteachgg$RIL[i])
}
p + xlab("Distance (cm)") + ylab("Probability density")
The last question involves checking that within-genotype heterogeneity exists by comparing AIC. First calculate summed AICs:
AIC_sums <- group_by(fiteachgg, RIL) %>%
summarize(AIC_sum = sum(AIC))
head(disperseRILgood) ID RIL Pot Distance Seedlings Siliques Height
1 2 3 0 4 85 111 19.8
2 2 3 1 8 14 111 19.8
3 2 3 1 9 15 111 19.8
4 2 3 1 10 11 111 19.8
5 2 3 1 11 13 111 19.8
6 2 3 1 12 12 111 19.8And now calculate the AICs of the homogeneous models for each RIL:
RIL_list <- levels(disperseRILgood$RIL)
fitall <- NULL
for (i in RIL_list) {
disperseRILi <- filter(disperseRILgood, RIL == i)
fitalli <- cbind(RIL = i,
fit_dispersal_untruncated(disperseRILi,
model = "gengamma",
control=controls))
fitall <- rbind(fitall, fitalli)
}And finally, the Delta-AICs:
fitall RIL ID model AIC par1 par2 par3 se1
1 3 2 gengamma 1496.9185 1.284194 0.8321789 0.6453752 0.09071515
2 18 7 gengamma 2331.9320 1.756110 0.7917102 1.0914188 0.07391116
3 22 11 gengamma 3737.0168 1.811838 0.6941734 1.4707358 0.05438901
4 35 17 gengamma 1152.8104 1.325718 0.7695415 0.6726952 0.09681197
5 42 23 gengamma 1648.7630 1.424013 0.7738100 1.0096373 0.07825046
6 53 29 gengamma 410.5883 1.057587 0.6246299 0.1559369 0.10387789
7 58 35 gengamma 429.7174 1.147355 0.7039492 0.2762669 0.12830943
8 101 41 gengamma 833.2313 1.297054 0.7165333 0.4399367 0.10354334
9 133 48 gengamma 223.4773 1.596692 0.3879342 2.4840639 0.14650906
10 144 53 gengamma 1195.8324 1.398686 0.8058324 0.7337590 0.09469582
11 147 59 gengamma 644.3591 1.516268 0.6968357 0.8841611 0.10464355
12 148 66 gengamma 233.3121 1.841793 0.5848407 2.0546329 0.24293039
13 180 73 gengamma 370.7943 1.216838 0.7196190 0.2632830 0.14464754
14 187 78 gengamma 488.9619 1.432784 0.8265801 0.4606547 0.15601217
se2 se3
1 0.03915775 0.1931607
2 0.03862401 0.1600287
3 0.03143665 0.1413259
4 0.04241569 0.2196602
5 0.03912494 0.1752732
6 0.04764835 0.2741321
7 0.05448401 0.3133580
8 0.04246512 0.2507517
9 0.10160535 0.8938374
10 0.04381724 0.2015363
11 0.05308896 0.2459684
12 0.15719974 0.8706514
13 0.06086707 0.3455521
14 0.06664233 0.3245522fitall$AIC - AIC_sums$AIC_sum [1] 11.0899832 28.0608487 43.5354532 31.3331529 23.6503093 14.8849572
[7] 5.2752959 -5.0652102 0.0000000 14.3740225 -4.4912259 -6.3239730
[13] 42.8189533 -0.5376814Positive values mean that the heterogeneous model is better. 9 RILs show strong evidence of heterogeneity; in 3 RILs the homogeneous model is better; in 2 the two models are indistinguishable.