How to get two random effects crossed with one nested in the other in nlme?

Question

My nonlinear mixed-effects model regresses body mass (bm) on age. I would like consider that brood is nested within year, but as a brood can only occur in one of the seven years that are in the dataset, the random effects of year and brood should be crossed.

In Pinheiro & Bates (2000): ‘Mixed-Effects Models in S and S-plus’ (http://link.springer.com/book/10.1007%2Fb98882), there is one example with crossed random effects: A full factorial model of a cell culture bioassay is used to represent the fixed effects, and three random effects are used to account for block, row, and column effects, with the last two random effects nested within block, but crossed with each other. This is implemented followingly (p. 163 - 165):

options( contrasts = c("contr.treatment", "contr.poly") )
fm1Assay <- lme( logDens ~ sample * dilut, Assay,
random = pdBlocked(list(pdIdent(~ 1), pdIdent(~ sample - 1), pdIdent(~ dilut - 1))) )

Their example is a linear mixed model, but the syntax should work also for nonlinear mixed models. Therefore, I tried the following for my model (I do not know however, why the nested effects have to have -1 after the covariate):

fmbm1 <- nlme(bm ~ SSlogis(age, Asym, xmid, scal), data = bmgrp,
             fixed = Asym + xmid + scal ~ 1, 
             random = pdBlocked(list(pdIdent(Asym + xmid + scal ~ 1),
                                pdIdent(Asym + xmid + scal ~ brood - 1))), 
             start = startvalues, na.action = na.omit)

But this syntax seems to be wrong, as it makes R freeze (there isn't even an error message, R just does not respond anymore so that I need to force quitting R). I would be happy about tips how to realise the nested and crossed structure in nlme.

Here is the structure of my data and below that the previous R code:

> str(bmgrp)
Classes ‘nfnGroupedData’, ‘nfGroupedData’, ‘groupedData’ and 'data.frame':  428 obs. of  7 variables:
 $ pop     : Factor w/ 2 levels "NL","RUS": 1 2 2 2 2 2 1 2 2 2 ...
 $ year    : Ord.factor w/ 7 levels "2013"<"2012"<..: 5 1 1 7 1 1 2 1 1 1 ...
 $ sex     : Factor w/ 2 levels "f","m": 2 1 1 2 1 2 1 2 1 2 ...
 $ age     : int  0 0 7 8 10 10 10 12 12 12 ...
 $ bm      : int  80 85 137 165 225 227 132 215 183 195 ...
 $ relhatch: num  4.06 4.22 4.22 4.29 1.22 ...
 $ brood   : Factor w/ 270 levels "","NL2004N1040054",..: 61 189 189 205 190 190 27 187 187 187 ...

bmdata <- read.table(header = TRUE, stringsAsFactors = TRUE, text = "
ID pop year sex age   bm     relhatch           brood
1    NL 2015   m   0   80   4.06293706      NL2015E278
2   RUS 2013   f   0   85   4.22000000     RUS2013N350
7   RUS 2013   f   7  137   4.21888412     RUS2013N350
9   RUS 2014   m   8  165   4.28608247    RUS2014N1372
11  RUS 2013   f  10  225   1.21888412     RUS2013N396
12  RUS 2013   m  10  227   1.21888412     RUS2013N396
13   NL 2012   f  10  132   0.86649874      NL2012E262
17  RUS 2013   m  12  215  -0.78111588     RUS2013N120
18  RUS 2013   f  12  183  -0.78111588     RUS2013N120
19  RUS 2013   m  12  195  -0.78111588     RUS2013N120
21  RUS 2014   m  13  325  -0.71391753     RUS2014N235
22  RUS 2014   m  13  280  -0.71391753     RUS2014N235
27  RUS 2013   m  16  498  -4.78111588      RUS2013N60
28  RUS 2005   m  17  870   3.20000000 RUS2005N1030701
29   NL 2012   m  18  324 -11.13350126       NL2012E45
32  RUS 2003   f  19  880   1.20000000 RUS2003N1030266
33  RUS 2005   f  19  750   6.10000000 RUS2005N1051002
35  RUS 2004   f  20  670   3.20000000 RUS2004N1030477
36  RUS 2004   m  20  790   3.20000000 RUS2004N1030491
37  RUS 2004   m  20  940   3.20000000 RUS2004N1030476
39  RUS 2004   f  20  900   3.20000000 RUS2004N1030521
40  RUS 2004   f  20  740   3.20000000 RUS2004N1030473
41  RUS 2003   m  21  980  -0.80000000 RUS2003N1030429
42   NL 2012   f  21  260  -2.13350126     NL2012Wun23
44  RUS 2014   m  21  620  -3.71391753     RUS2014N248
45  RUS 2003   m  21 1080  -0.80000000 RUS2003N1030045
46   NL 2012   m  21  237  -0.13350126      NL2012E265
47  RUS 2004   m  21  572   2.80000000 RUS2004N1040648
48  RUS 2004   m  21  940   3.20000000 RUS2004N1030482
49  RUS 2004   m  21  450   4.20000000 RUS2004N1030645
53  RUS 2014   f  22  660  -0.71391753     RUS2014N866
54  RUS 2003   f  22  890  -1.80000000 RUS2003N1030415
55  RUS 2005   f  22  684   0.80000000 RUS2005N1040060
56  RUS 2005   f  22  652   0.80000000 RUS2005N1040060
57  RUS 2003   f  22  776  -1.80000000 RUS2003N1030418
58  RUS 2004   m  22  672   1.80000000 RUS2004N1042138
59  RUS 2004   f  22  622   1.80000000 RUS2004N1042138
61  RUS 2004   m  22  472   3.30000000 RUS2004N1042092
62  RUS 2004   f  22  438   3.30000000 RUS2004N1042092
63   NL 2012   m  22  222   7.86649874      NL2012W213
64  RUS 2003   m  22 1410  -1.80000000 RUS2003N1030417
65  RUS 2003   f  22 1010  -1.80000000 RUS2003N1030089
66  RUS 2004   f  22  612   1.20000000 RUS2004N1030470
67  RUS 2004   m  22  598   1.80000000 RUS2004N1042139
68  RUS 2004   f  22  316   1.30000000 RUS2004N1042114
69  RUS 2004   m  22  420   3.20000000 RUS2004N1030474
70  RUS 2004   m  22  370   3.30000000 RUS2004N1042095
76  RUS 2004   f  23 1080   0.20000000 RUS2004N1030467
77  RUS 2003   f  23  854  -2.80000000 RUS2003N1030196
78  RUS 2003   f  23  897  -1.80000000 RUS2003N1030402
79  RUS 2003   m  23 1210  -1.80000000 RUS2003N1030416
80  RUS 2003   f  23 1180  -1.80000000 RUS2003N1030416
81  RUS 2004   m  23  990   0.20000000 RUS2004N1030446
82  RUS 2004   f  23  990   0.20000000 RUS2004N1030446
83  RUS 2004   f  23 1110   0.20000000 RUS2004N1030461
84  RUS 2014   m  23  710  -5.71391753     RUS2014N160
85  RUS 2014   f  23  695  -1.71391753     RUS2014N600
86  RUS 2003   m  23 1230  -1.80000000 RUS2003N1030404
87  RUS 2004   m  23  870   0.20000000 RUS2004N1030465
88  RUS 2004   f  23  500   0.80000000 RUS2004N1040578
89  RUS 2004   m  23  598   0.80000000 RUS2004N1040288
90  RUS 2004   f  23  480   2.80000000 RUS2004N1040685
91  RUS 2004   m  23  444   2.80000000 RUS2004N1040688
92  RUS 2005   f  23  820  -0.80000000 RUS2005N1030706
99  RUS 2004   m  24 1120  -0.80000000 RUS2004N1030467
100 RUS 2004   m  24  612  -0.20000000 RUS2004N1040474
101 RUS 2004   m  24  642  -0.20000000 RUS2004N1040474
102 RUS 2004   m  24  634  -0.20000000 RUS2004N1040474
103 RUS 2014   f  24  740   2.28608247      RUS2014N49
104 RUS 2014   f  24  840   2.28608247      RUS2014N49
105 RUS 2014   m  24  900   2.28608247      RUS2014N49
106 RUS 2005   m  24  972   0.80000000 RUS2005N1040106
107 RUS 2005   f  24  820   0.80000000 RUS2005N1040106
108 RUS 2005   f  24  910   0.80000000 RUS2005N1040106
109 RUS 2014   m  24  980   2.28608247     RUS2014N759
110 RUS 2014   f  24  775   2.28608247     RUS2014N759
111 RUS 2004   f  24  870   0.20000000 RUS2004N1030457
112 RUS 2004   f  24  516   0.80000000 RUS2004N1040528
113 RUS 2004   f  24  672   1.80000000 RUS2004N1040828
114 RUS 2004   f  24  604   1.80000000 RUS2004N1040828
115 RUS 2004   m  24  790   3.20000000 RUS2004N1030491
116 RUS 2004   m  24  940   3.20000000 RUS2004N1030487
117 RUS 2004   m  24 1040   3.20000000 RUS2004N1030487
118  NL 2015   m  24  300   4.06293706      NL2015E278
119  NL 2012   m  24  258  -8.13350126      NL2012Eun7
120  NL 2012   f  24  190   3.86649874      NL2012E239
121 RUS 2014   m  24 1085   2.28608247     RUS2014N858
122 RUS 2003   m  24 1100   1.20000000 RUS2003N1030333
123 RUS 2004   m  24  610  -0.70000000 RUS2004N1040622
124 RUS 2004   m  24  674  -0.20000000 RUS2004N1040444
125 RUS 2004   m  24  772  -0.20000000 RUS2004N1040285
126 RUS 2004   m  24  760  -0.20000000 RUS2004N1040571
127 RUS 2005   m  24 1060   0.80000000 RUS2005N1040118
139 RUS 2014   f  25  860   4.28608247     RUS2014N766
140 RUS 2014   m  25 1040   4.28608247     RUS2014N766
142  NL 2015   f  25  490  -0.93706294      NL2015W224
143 RUS 2014   m  25 1002   1.28608247      RUS2014NT1
144 RUS 2014   f  25  880   1.28608247     RUS2014N812
145 RUS 2014   m  25  955   1.28608247     RUS2014N111
146 RUS 2014   m  25  985   1.28608247     RUS2014N111
147 RUS 2003   f  25  980  -0.80000000 RUS2003N1030045
148 RUS 2004   f  25 1070   0.20000000 RUS2004N1030466
149 RUS 2004   m  25 1050   0.20000000 RUS2004N1030439
150 RUS 2004   f  25  940   0.20000000 RUS2004N1030439
151 RUS 2004   f  25  900   0.20000000 RUS2004N1030461
152 RUS 2014   m  25  985   1.28608247     RUS2014N602
153 RUS 2004   m  25  560  -1.20000000 RUS2004N1040503
154 RUS 2004   f  25  680   0.20000000 RUS2004N1030437
155 RUS 2004   f  25  910   0.20000000 RUS2004N1030451
156 RUS 2004   m  25  484   0.80000000 RUS2004N1040541
158 RUS 2014   f  26  985   0.28608247      RUS2014N61
159 RUS 2014   f  26  882   0.28608247      RUS2014N61
160 RUS 2004   m  26  626  -0.20000000 RUS2004N1040474
161 RUS 2003   f  26  900  -0.80000000 RUS2003N1030429
162 RUS 2004   m  26  810   3.20000000 RUS2004N1030476
163 RUS 2014   f  26  860   0.28608247     RUS2014N706
164 RUS 2014   f  26  945   2.28608247     RUS2014N963
165  NL 2004   f  26  480  23.00000000  NL2004N1040293
166 RUS 2004   f  26  720  -0.70000000 RUS2004N1040832
167 RUS 2004   m  26  658   1.30000000 RUS2004N1042086
168 RUS 2004   f  26  634   1.80000000 RUS2004N1042149
171 RUS 2004   f  27 1300  -1.80000000 RUS2004N1030455
172 RUS 2014   f  27  800  -0.71391753     RUS2014N619
173 RUS 2014   m  27 1020  -0.71391753     RUS2014N411
174 RUS 2014   m  27 1040  -0.71391753     RUS2014N411
175 RUS 2014   f  27  980   3.28608247    RUS2014N1119
176 RUS 2014   m  27  990   3.28608247    RUS2014N1119
177 RUS 2014   m  27  925   3.28608247    RUS2014N1119
178 RUS 2003   f  27  762  -1.80000000 RUS2003N1030400
179 RUS 2003   f  27  880  -1.80000000 RUS2003N1030415
180 RUS 2003   f  27 1020  -1.80000000 RUS2003N1030406
181 RUS 2003   f  27  950  -1.80000000 RUS2003N1030406
182 RUS 2003   m  27 1060  -1.80000000 RUS2003N1030406
183 RUS 2003   m  27  772   0.20000000 RUS2003N1030400
184  NL 2015   m  27  525   1.06293706      NL2015E222
185 RUS 2014   f  27  830   2.28608247     RUS2014N769
186 RUS 2014   f  27  940   2.28608247     RUS2014N769
187 RUS 2003   m  27  976  -1.80000000 RUS2003N1030402
188 RUS 2003   f  27 1050  -1.80000000 RUS2003N1030413
189 RUS 2003   m  27 1090  -1.80000000 RUS2003N1030414
190 RUS 2003   f  27 1140  -1.80000000 RUS2003N1030413
191 RUS 2003   f  27 1080  -1.80000000 RUS2003N1030414
192 RUS 2004   f  27  630   3.20000000 RUS2004N1030475
193  NL 2012   m  27  290   0.86649874      NL2012W103
194 RUS 2014   m  27 1100  -0.71391753     RUS2014N519
195 RUS 2014   m  27  985  -0.71391753     RUS2014N629
196 RUS 2014   m  27  925   1.28608247     RUS2014N533
197 RUS 2014   f  27  950   2.28608247     RUS2014N452
198 RUS 2003   f  27 1060  -1.80000000 RUS2003N1030411
199 RUS 2005   f  27  990   3.10000000 RUS2005N1050621
204  NL 2012   f  28  237  -0.13350126      NL2012E262
206 RUS 2014   m  28 1085  -1.71391753     RUS2014N321
207 RUS 2014   m  28 1220  -1.71391753     RUS2014N321
208 RUS 2014   m  28 1010  -1.71391753     RUS2014N321
209 RUS 2014   f  28 1005   2.28608247     RUS2014N554
210 RUS 2014   m  28 1040   2.28608247     RUS2014N554
211 RUS 2014   f  28 1005   2.28608247     RUS2014N554
212 RUS 2003   f  28  960  -0.80000000 RUS2003N1030429
213 RUS 2003   m  28 1330  -0.80000000 RUS2003N1030100
214 RUS 2003   f  28 1140  -0.80000000 RUS2003N1030100
215 RUS 2003   m  28 1340  -0.80000000 RUS2003N1030100
216 RUS 2004   m  28  586  -2.20000000 RUS2004N1040279
217 RUS 2005   m  28  894   0.80000000 RUS2005N1040060
218 RUS 2014   m  28  980  -1.71391753     RUS2014N631
219 RUS 2014   f  28  790   1.28608247      RUS2014NT1
220 RUS 2003   f  28  902  -2.80000000 RUS2003N1030196
221 RUS 2004   f  28  744  -3.20000000 RUS2004N1040600
222 RUS 2005   m  28  576   0.80000000 RUS2005N1040130
223 RUS 2005   f  28  517   0.80000000 RUS2005N1040130
224 RUS 2014   f  28  855   2.28608247    RUS2014N1171
225 RUS 2003   f  28  740  -0.80000000 RUS2003N1030090
226 RUS 2004   m  28  792  -2.20000000 RUS2004N1040381
227 RUS 2005   m  28 1034   0.80000000 RUS2005N1040265
231  NL 2015   f  29  430  -0.93706294      NL2015W228
232  NL 2015   f  29  425  -0.93706294      NL2015W228
233 RUS 2014   m  29  843  -2.71391753     RUS2014N418
234 RUS 2014   f  29 1020  -2.71391753     RUS2014N418
235 RUS 2014   m  29 1100  -4.71391753     RUS2014N123
236 RUS 2014   f  29 1100  -4.71391753     RUS2014N123
237 RUS 2014   m  29 1000  -2.71391753     RUS2014N113
238 RUS 2014   m  29 1160  -2.71391753     RUS2014N113
239 RUS 2014   f  29 1000  -2.71391753     RUS2014N113
240 RUS 2014   f  29 1055  -2.71391753     RUS2014N286
241 RUS 2014   f  29 1100  -2.71391753     RUS2014N286
242 RUS 2014   f  29 1125  -0.71391753      RUS2014NT7
243 RUS 2014   f  29  985  -0.71391753     RUS2014N284
244 RUS 2004   f  29  612   0.80000000 RUS2004N1040528
245 RUS 2005   m  29  624  -0.20000000 RUS2005N1040150
246 RUS 2005   f  29  510  -0.20000000 RUS2005N1040150
247 RUS 2005   m  29 1000  -0.20000000 RUS2005N1040151
248 RUS 2005   f  29  902  -0.20000000 RUS2005N1040151
249 RUS 2014   f  29 1115  -2.71391753     RUS2014N672
250 RUS 2014   f  29 1245  -0.71391753     RUS2014N616
251 RUS 2014   m  29 1325  -0.71391753     RUS2014N239
252 RUS 2004   f  29  860   3.20000000 RUS2004N1030484
253 RUS 2005   m  29  708  -0.70000000 RUS2005N1040163
254 RUS 2005   m  29  618  -0.20000000 RUS2005N1040082
255 RUS 2005   f  29  910  -0.20000000 RUS2005N1040137
264 RUS 2014   m  30 1170   0.28608247      RUS2014N61
265 RUS 2004   f  30 1090   0.20000000 RUS2004N1030467
266 RUS 2014   f  30 1030  -0.71391753     RUS2014N866
267 RUS 2014   m  30 1025  -0.71391753     RUS2014N619
268 RUS 2014   m  30 1120   7.28608247    RUS2014N1016
269 RUS 2014   f  30 1000   7.28608247    RUS2014N1016
270 RUS 2014   f  30  890   7.28608247    RUS2014N1016
271 RUS 2004   m  30  954  -2.20000000 RUS2004N1040606
272 RUS 2004   f  30  965  -2.20000000 RUS2004N1040606
273 RUS 2004   m  30  948  -2.20000000 RUS2004N1040606
274 RUS 2005   m  30 1238  -1.20000000 RUS2005N1040217
275 RUS 2005   m  30 1260  -1.20000000 RUS2005N1040217
276 RUS 2005   f  30 1146  -1.20000000 RUS2005N1040217
277 RUS 2014   m  30 1182  -3.71391753     RUS2014N112
279 RUS 2014   m  30 1260  -3.71391753     RUS2014N112
281 RUS 2014   f  30 1200  -3.71391753     RUS2014N364
282 RUS 2014   m  30 1110  -0.71391753     RUS2014N221
283 RUS 2014   m  30 1235  -0.71391753     RUS2014N221
284 RUS 2004   m  30  880   0.20000000 RUS2004N1030442
285 RUS 2004   f  30  720   0.20000000 RUS2004N1030442
286 RUS 2014   m  30 1022  -3.71391753     RUS2014N238
287 RUS 2014   m  30 1120  -3.71391753     RUS2014N270
288 RUS 2014   m  30 1175  -3.71391753     RUS2014N647
289 RUS 2014   f  30 1100  -3.71391753     RUS2014N288
290 RUS 2014   f  30  980   1.28608247    RUS2014N1032
291 RUS 2004   f  30  840   0.20000000 RUS2004N1030449
292 RUS 2005   m  30 1080  -1.40000000 RUS2005N1050085
294  NL 2012   f  31  430  -3.13350126       NL2012W27
295  NL 2012   m  31  405  -3.13350126       NL2012W27
296  NL 2015   m  31  810  -2.93706294      NL2015E149
297  NL 2015   m  31  740  -2.93706294      NL2015E149
298 RUS 2014   f  31 1140  -0.71391753     RUS2014N914
299 RUS 2014   m  31 1255  -0.71391753     RUS2014N914
300 RUS 2014   f  31 1225  -0.71391753     RUS2014N914
301 RUS 2014   m  31 1020  -0.71391753     RUS2014N411
302 RUS 2014   m  31 1255   2.28608247     RUS2014N698
303 RUS 2014   m  31 1235   2.28608247     RUS2014N698
304 RUS 2014   m  31 1120   2.28608247     RUS2014N698
305 RUS 2004   m  31 1204  -0.70000000 RUS2004N1040833
306 RUS 2004   f  31 1024  -0.70000000 RUS2004N1040833
307 RUS 2004   m  31  790   3.20000000 RUS2004N1030475
308 RUS 2004   m  31  824   1.30000000 RUS2004N1042120
309 RUS 2004   f  31  704   1.30000000 RUS2004N1042142
318  NL 2012   f  32  418  -4.13350126       NL2012W70
319  NL 2012   m  32  410  -4.13350126       NL2012W70
320 RUS 2004   m  32 1340  -1.80000000 RUS2004N1030455
321 RUS 2005   f  32 1140   2.10000000 RUS2005N1050173
322 RUS 2005   m  32 1330   2.10000000 RUS2005N1050173
323 RUS 2005   m  32 1300   2.10000000 RUS2005N1050173
324 RUS 2005   m  32 1210   2.10000000 RUS2005N1050173
325 RUS 2005   f  32 1070   2.10000000 RUS2005N1050173
326  NL 2015   m  32  810  -3.93706294       NL2015W40
327  NL 2012   m  32  408  -4.13350126       NL2012E25
328  NL 2012   f  32  282  -4.13350126       NL2012E25
330 RUS 2005   f  32 1050   2.10000000 RUS2005N1050505
331 RUS 2005   f  32 1050   2.10000000 RUS2005N1050505
332 RUS 2005   f  32  930   2.10000000 RUS2005N1050505
333 RUS 2014   f  32 1125  -3.71391753      RUS2014N91
334 RUS 2014   m  32 1402  -3.71391753      RUS2014N91
335 RUS 2014   f  32 1085  -1.71391753     RUS2014N631
336 RUS 2003   f  32 1140  -0.80000000 RUS2003N1030424
337 RUS 2003   m  32 1100  -0.80000000 RUS2003N1030424
338 RUS 2004   m  32 1010   0.20000000 RUS2004N1030457
339 RUS 2005   m  32 1008  -3.20000000 RUS2005N1040180
340 RUS 2005   f  32  830  -3.20000000 RUS2005N1040180
342 RUS 2014   f  32 1140  -5.71391753     RUS2014N117
343  NL 2004   f  32  530  17.50000000  NL2004N1041011
344 RUS 2004   f  32  640   0.20000000 RUS2004N1030459
348 RUS 2014   m  33 1265  -3.71391753     RUS2014N293
349 RUS 2014   m  33 1190  -3.71391753     RUS2014N293
350 RUS 2014   m  33 1225  -3.71391753     RUS2014N293
351 RUS 2014   f  33 1090  -3.71391753     RUS2014N293
352 RUS 2004   m  33 1160  -0.80000000 RUS2004N1030467
354 RUS 2003   m  33  980  -1.80000000 RUS2003N1030415
355 RUS 2004   f  33  476  -2.20000000 RUS2004N1040279
356 RUS 2004   m  33  554  -2.20000000 RUS2004N1040279
357 RUS 2014   f  33 1310   4.28608247    RUS2014N1000
358 RUS 2014   f  33 1060   4.28608247    RUS2014N1000
359 RUS 2003   m  33  842  -1.80000000 RUS2003N1030418
360 RUS 2005   m  33 1050  -2.90000000 RUS2005N1050580
361 RUS 2005   m  33 1226  -2.90000000 RUS2005N1050580
362 RUS 2014   m  33 1190  -2.71391753     RUS2014N175
363 RUS 2014   f  33 1105   4.28608247     RUS2014N755
364 RUS 2014   m  33 1260   4.28608247     RUS2014N801
365 RUS 2003   f  33  850  -1.80000000 RUS2003N1030422
367 RUS 2004   m  33 1054  -2.20000000 RUS2004N1040478
368 RUS 2004   f  33  810   0.20000000 RUS2004N1030456
369 RUS 2004   m  33  944   1.80000000 RUS2004N1041049
370 RUS 2004   m  33 1102   1.30000000 RUS2004N1042127
371 RUS 2004   f  33 1050   1.80000000 RUS2004N1040821
372 RUS 2004   f  33  935   1.80000000 RUS2004N1042131
373 RUS 2005   m  33  868  -4.20000000 RUS2005N1040266
376  NL 2012   m  34  270  -6.13350126       NL2012W15
377  NL 2012   f  34  438  -6.13350126       NL2012W15
379  NL 2012   m  34  440  -6.13350126     NL2012Wun15
380  NL 2012   f  34  440  -6.13350126     NL2012Wun15
383 RUS 2014   f  34  990  -4.71391753     RUS2014N216
384 RUS 2014   f  34 1220  -3.71391753     RUS2014N106
385 RUS 2014   f  34 1090  -3.71391753     RUS2014N106
386 RUS 2014   m  34 1240  -0.71391753      RUS2014NT7
387 RUS 2014   f  34 1085   3.28608247     RUS2014N896
388 RUS 2014   m  34 1110   3.28608247     RUS2014N896
389 RUS 2004   m  34 1074  -1.20000000 RUS2004N1040269
390 RUS 2004   f  34  980  -1.20000000 RUS2004N1040269
391 RUS 2004   f  34  930   0.20000000 RUS2004N1030466
392 RUS 2004   f  34 1042  -3.20000000 RUS2004N1040455
393 RUS 2004   m  34  815   0.80000000 RUS2004N1040516
399 RUS 2014   m  35 1275  -1.71391753     RUS2014N332
400 RUS 2014   f  35 1210  -1.71391753     RUS2014N332
401 RUS 2014   m  35 1230  -1.71391753     RUS2014N332
402 RUS 2014   m  35 1380   2.28608247     RUS2014N733
403 RUS 2014   m  35 1410   2.28608247     RUS2014N733
404 RUS 2014   f  35 1270   2.28608247     RUS2014N733
405 RUS 2014   f  35 1040   2.28608247    RUS2014N1102
406 RUS 2014   f  35 1080   2.28608247    RUS2014N1102
407 RUS 2005   f  35 1150  -0.90000000 RUS2005N1051024
408 RUS 2005   m  35 1390  -0.90000000 RUS2005N1051024
409  NL 2012   m  35  455  -7.13350126      NL2012E121
410 RUS 2014   m  35 1250  -3.71391753     RUS2014N397
411  NL 2005   m  35  990   1.30000000  NL2005N1050244
412 RUS 2004   f  35 1020  -2.20000000 RUS2004N1040437
413 RUS 2005   m  35 1200  -6.40000000 RUS2005N1050422
418 RUS 2004   m  36 1320  -1.80000000 RUS2004N1030455
419 RUS 2004   m  36 1270  -1.80000000 RUS2004N1030455
420 RUS 2004   m  36 1430  -1.80000000 RUS2004N1030455
421  NL 2012   f  36  460  -8.13350126      NL2012Wun5
422  NL 2012   m  36  505  -8.13350126      NL2012Wun5
424 RUS 2004   m  36  916  -3.20000000 RUS2004N1040600
425 RUS 2014   m  36 1300   1.28608247    RUS2014N1451
426 RUS 2005   m  36 1420  -1.40000000 RUS2005N1050054
427 RUS 2005   f  36 1170  -1.90000000 RUS2005N1050270
432 RUS 2013   f  37 1030  -4.78111588     RUS2013N407
433 RUS 2013   f  37 1050  -4.78111588     RUS2013N407
434 RUS 2013   m  37 1140  -4.78111588     RUS2013N407
439 RUS 2014   f  37 1250   0.28608247     RUS2014N422
440 RUS 2004   f  37 1120  -2.20000000 RUS2004N1040480
447 RUS 2014   m  38 1615  -4.71391753     RUS2014N351
448 RUS 2014   f  38 1430  -4.71391753     RUS2014N351
449 RUS 2014   f  38 1225  -0.71391753     RUS2014N386
450 RUS 2014   f  38 1315  -0.71391753     RUS2014N386
451  NL 2015   m  38  940  -2.93706294      NL2015E117
452  NL 2012   m  38 1090  -5.13350126      NL2012E130
453 RUS 2014   f  38 1225  -0.71391753     RUS2014N668
454 RUS 2014   m  38 1430  -0.71391753     RUS2014N493
461  NL 2012   f  39  535 -11.13350126       NL2012E31
462  NL 2012   f  39  195 -11.13350126      NL2012Wun1
463 RUS 2014   m  39 1440  -1.71391753     RUS2014N202
464 RUS 2014   m  39 1250  -1.71391753     RUS2014N202
465  NL 2015   m  39  600   2.06293706      NL2015W280
466  NL 2012   f  39 1090  16.86649874      NL2012E323
467 RUS 2014   f  39 1325  -1.71391753     RUS2014N266
468  NL 2004   m  39 1050   9.00000000  NL2004N1040299
475 RUS 2014   m  40 1480  -2.71391753     RUS2014N300
476 RUS 2014   m  40 1450  -2.71391753     RUS2014N300
477 RUS 2014   m  40 1475  -2.71391753     RUS2014N300
478 RUS 2014   f  40 1230  -2.71391753     RUS2014N656
479 RUS 2014   f  40 1300  -2.71391753     RUS2014N207
480 RUS 2014   m  40 1480  -2.71391753     RUS2014N207
481 RUS 2014   m  40 1310  -2.71391753     RUS2014N656
482  NL 2012   m  40  805  -8.13350126       NL2012W39
483 RUS 2014   m  40 1428  -2.71391753     RUS2014N273
491 RUS 2014   m  41 1110  -3.71391753     RUS2014N615
492  NL 2004   f  41 1000   7.00000000  NL2004N1040255
502  NL 2012   f  44  700  -6.13350126       NL2012W15
503  NL 2005   m  44 1160  -7.20000000  NL2005N1050197
504  NL 2005   m  44 1020  -7.20000000  NL2005N1050197
505  NL 2005   m  44 1240  -7.20000000  NL2005N1050197
506  NL 2005   f  44 1050  -7.20000000  NL2005N1050197
508  NL 2012   m  45  710  -7.13350126        NL2012W9
509  NL 2012   f  45  680  -7.13350126        NL2012W9
510  NL 2012   m  47 1100  -2.13350126      NL2012W154
511  NL 2015   m  47  630  -5.93706294      NL2015W202
512  NL 2012   m  47 1130  -2.13350126      NL2012E197
513  NL 2004   f  47 1210   1.00000000  NL2004N1040149
514  NL 2004   f  47 1250   1.00000000  NL2004N1040157
519  NL 2004   f  50 1320  -2.00000000  NL2004N1040129
520  NL 2004   m  50 1380  -2.00000000  NL2004N1040129
521  NL 2012   f  50 1060  -8.13350126      NL2012E111
522  NL 2004   m  50 1510  -2.00000000  NL2004N1040119
523  NL 2004   f  50  940  -1.50000000  NL2004N1040102
524  NL 2012   m  51  625  -3.13350126       NL2012W27
525  NL 2012   f  51 1325  -6.13350126       NL2012E28
527  NL 2012   f  52 1220  -1.13350126      NL2012E154
528  NL 2004   m  52 1160  -5.00000000  NL2004N1040134
529  NL 2012   m  53 1200  -2.13350126      NL2012W154
530  NL 2012   f  53  880  -5.13350126      NL2012Wun9
531  NL 2012   f  53  880  -5.13350126      NL2012Wun9
532  NL 2004   m  53 1290  -5.00000000  NL2004N1040106
533  NL 2004   m  53 1230  -5.00000000  NL2004N1040106
534  NL 2012   m  53  790  -5.13350126     NL2012Wun12
535  NL 2012   m  53 1130  -2.13350126       NL2012W57
536  NL 2012   f  53 1300   2.86649874     NL2012Wun24
537  NL 2004   m  53 1530  -5.00000000  NL2004N1040063
538  NL 2004   m  54 1450  -5.00000000  NL2004N1040054
539  NL 2004   m  54 1060  -5.00000000  NL2004N1040054
540  NL 2004   f  54 1110  -5.00000000  NL2004N1040054
541  NL 2012   f  54  695  -6.13350126      NL2012E131
542  NL 2012   m  54  935  -6.13350126      NL2012W115
543  NL 2012   f  54  640  -6.13350126      NL2012E131
544  NL 2012   f  54  830  -6.13350126      NL2012W115
545  NL 2004   m  54 1380  -5.00000000  NL2004N1040057
546  NL 2004   f  54  910  -5.00000000  NL2004N1041151
550  NL 2012   m  56 1325 -11.13350126       NL2012E45
551  NL 2012   m  56  900  -5.13350126       NL2012E32
552  NL 2012   f  56 1225  -5.13350126       NL2012E32
553  NL 2015   m  56 1510   0.06293706      NL2015E209
554  NL 2012   f  56 1280  -3.13350126      NL2012W203
555  NL 2012   f  57 1180  -4.13350126       NL2012E25
556  NL 2015   m  57 1180  -7.93706294        NL2015Wu
557  NL 2015   f  57 1080  -0.93706294      NL2015W348
559  NL 2015   f  58  980  -1.93706294       NL2015E93
560  NL 2015   f  58 1040  -1.93706294        NL2015Eu
562  NL 2015   f  59 1040  -2.93706294      NL2015W216
563  NL 2015   f  59 1030  -2.93706294      NL2015W216
564  NL 2015   f  59 1140  -2.93706294      NL2015W216
565  NL 2015   m  59 1440  -2.93706294       NL2015E66
566  NL 2012   f  59 1360  -8.13350126       NL2012W35
567  NL 2012   m  60 1070 -15.13350126       NL2012W49
569  NL 2012   m  62 1400 -11.13350126       NL2012E37")

bmgrp   <- groupedData(bm   ~ age | year, data = bmdata)
options(contrasts = c("contr.sum","contr.poly"))
contrasts(bmgrp$pop); contrasts(bmgrp$sex)
startvalues <- c(31.228925, 75.552237, 12.708210, 9.427097)

Answer 1

Some further search in the internet brought me to the following article: Zhou et al. (2007): Using a nonlinear crossed random effects model for describing circadian patterns of serum prolactin concentrations in heat stressed Holsteins (http://newprairiepress.org/cgi/viewcontent.cgi?article=1113&context=agstatconference). They write the following about crossed random effects in nlme:
Fitting nonlinear mixed models with both crossed and nested random effects is still a new and challenging topic in statistics. […] The NLME package in R is very powerful for fitting multilevel nonlinear mixed-effects models with nested random effects, but it does not fit nonlinear mixed-effects models with crossed random effects (Pinheiro and Bates, 2000). Rasbash and Goldstein (1994) show how to fit a linear mixed model with crossed random effects as a purely hierarchical formulation of nested random effects. Zhou, Parkhurst, et al (2006) (http://newprairiepress.org/agstatconference/2006/proceedings/11/) developed a method to enable NLME in R to fit a nonlinear mixed-effects model with crossed random effects based on Rasbash and Goldstein’s idea for linear mixed-effects model. This method can be used to fit a nonlinear mixed effects model with arbitrary levels of crossed and nested random effects. However, only one correlation for the crossed random effects can be estimated. The NLME code for fitting the nonlinear mixed-effects model […] is documented in the Appendix.

# Feeding Event is specified as the lowest hierarchical level grouping factor
# (hierarchical level 1 grouping factor)
# Specify Pig as a standard hierarchical level 2 grouping factor
# Create a new grouping factor as the highest hierarchical level
# (hierarchical level 3 grouping factor) with one level spanning the entire data set
newGF <- factor(rep(1,length(heat$Y)))
# Specify that each level of Period has a coefficient random at newGF
# “ -1” indicates that the specific term factor(Period ) does not have an intercept
# It is not possible to estimate the correlation associated with Period.

full.nlme <-
nlme(model = Y ~ Y0 + KG * (exp(-KD * X) - exp(-KG * X))/(KG - KD),
fixed = Y0 + KG + KD ~ factor(Trt),
random = list(newGF = pdIdent(Y0 ~ factor(Period) -1),
newGF = pdIdent(KG ~ factor(Period) -1),
newGF = pdIdent(KD ~ factor(Period) -1),
Pig = pdDiag(Y0 + KG + KD ~ 1),
Event = pdDiag(Y0 + KG + KD ~ 1)),
start = c(39, 0, 0, 60, 0, 0, 20, 0, 0), data = heat)

I applied this syntax to my case - and it worked! Here it is:

fmbm1 <- nlme(bm ~ SSlogis(age, Asym, xmid, scal), data = bmgrp,
             fixed = Asym + xmid + scal ~ 1, 
             random = list(dummy = pdIdent(Asym ~ factor(year) - 1),
                           dummy = pdIdent(xmid ~ factor(year) - 1),
                           dummy = pdIdent(scal ~ factor(year) - 1),
                           brood = pdDiag(Asym + xmid + scal ~ 1)), 
             start = coef(fmbml), na.action = na.omit)

> summary(fmbm1)
Nonlinear mixed-effects model fit by maximum likelihood
  Model: bm ~ SSlogis(age, Asym, xmid, scal) 
 Data: bmgrp 
       AIC      BIC    logLik
  5505.905 5546.235 -2742.952

Random effects:
 Formula: Asym ~ factor(year) - 1 | dummy
 Structure: Multiple of an Identity
        Asym.factor(year)2013 Asym.factor(year)2012 Asym.factor(year)2003 Asym.factor(year)2005 Asym.factor(year)2015 Asym.factor(year)2004
StdDev:           0.004011662           0.004011662           0.004011662           0.004011662           0.004011662           0.004011662
        Asym.factor(year)2014
StdDev:           0.004011662

 Formula: xmid ~ factor(year) - 1 | dummy %in% dummy
 Structure: Multiple of an Identity
        xmid.factor(year)2013 xmid.factor(year)2012 xmid.factor(year)2003 xmid.factor(year)2005 xmid.factor(year)2015 xmid.factor(year)2004
StdDev:              8.630687              8.630687              8.630687              8.630687              8.630687              8.630687
        xmid.factor(year)2014
StdDev:              8.630687

 Formula: scal ~ factor(year) - 1 | dummy %in% dummy %in% dummy
 Structure: Multiple of an Identity
        scal.factor(year)2013 scal.factor(year)2012 scal.factor(year)2003 scal.factor(year)2005 scal.factor(year)2015 scal.factor(year)2004
StdDev:              1.890416              1.890416              1.890416              1.890416              1.890416              1.890416
        scal.factor(year)2014
StdDev:              1.890416

 Formula: list(Asym ~ 1, xmid ~ 1, scal ~ 1)
 Level: brood %in% dummy %in% dummy %in% dummy
 Structure: Diagonal
                Asym     xmid        scal Residual
StdDev: 2.176433e-05 5.079293 0.001926683 99.83194

Fixed effects: Asym + xmid + scal ~ 1 
                     Value Std.Error  DF   t-value p-value
Asym.(Intercept) 1721.7518 123.05426 153 13.991810       0
xmid.(Intercept)   32.1919   3.83007 153  8.405047       0
scal.(Intercept)   11.5256   1.36451 153  8.446679       0
 Correlation: 
                 As.(I) xm.(I)
xmid.(Intercept) 0.495        
scal.(Intercept) 0.734  0.369 

Standardized Within-Group Residuals:
        Min          Q1         Med          Q3         Max 
-2.20621393 -0.43418898  0.01076569  0.40318446  2.34353430 

Number of Observations: 417
Number of Groups: 
                                     dummy                         dummy.1 %in% dummy            dummy.2 %in% dummy.1 %in% dummy 
                                         1                                          1                                          1 
brood %in% dummy.2 %in% dummy.1 %in% dummy 
                                       262 
>