Dear All, I would like to ask a couple of questions on a LME model. I tested 4 selection lines at 4 food concentrations against a standard competitor stock. I had 3 replicate cages per selection line. In each cage I have 10 vials. I counted the number of wild type flies and competitor stock emerging in each vial. My main question is: is there any difference between selection lines? I did fit the following model: mod1<-lme(wt~selection*food, random=~1|c1/food, competition) The quantile plot is straight, the plot of residuals looks good, the standardized residual plot seems ok... BUT if I do a bartlett test for homogeneity of variance (done by cage*temperature, 48 cages in all) the variance is NOT homogeneous. Is my model still accettable? if not, what could I do? The same model on asin(sqrt(wild type/total)) does not fit anywhere as well. my dataset (NB *wt* is the number of wild type flies in each vial; *spa* is the number of comepetitor stock flies in each vial, *p1* is asin(sqrt(competition$prop)), *c1* is the cage nested in selection using getGroups...): selection cage food wt spa tot prop p1 c1 1 25 1 100 21 22 43 0.48837209 0.7737692 25/1 2 25 1 100 21 22 43 0.48837209 0.7737692 25/1 3 25 1 100 5 5 10 0.50000000 0.7853982 25/1 4 25 1 100 21 17 38 0.55263158 0.8381274 25/1 5 25 1 100 13 22 35 0.37142857 0.6553659 25/1 6 25 1 100 24 18 42 0.57142857 0.8570719 25/1 7 25 1 100 22 19 41 0.53658537 0.8220163 25/1 8 25 1 100 15 23 38 0.39473684 0.6793415 25/1 9 25 1 100 19 19 38 0.50000000 0.7853982 25/1 10 25 1 100 18 19 37 0.48648649 0.7718830 25/1 11 25 2 100 21 22 43 0.48837209 0.7737692 25/2 12 25 2 100 24 18 42 0.57142857 0.8570719 25/2 13 25 2 100 9 21 30 0.30000000 0.5796397 25/2 14 25 2 100 2 13 15 0.13333333 0.3737922 25/2 15 25 2 100 10 11 21 0.47619048 0.7615796 25/2 16 25 2 100 26 20 46 0.56521739 0.8508019 25/2 17 25 2 100 11 17 28 0.39285714 0.6774179 25/2 18 25 2 100 9 22 31 0.29032258 0.5690309 25/2 19 25 2 100 15 22 37 0.40540541 0.6902300 25/2 20 25 2 100 19 24 43 0.44186047 0.7271268 25/2 21 25 3 100 22 23 45 0.48888889 0.7742861 25/3 22 25 3 100 13 22 35 0.37142857 0.6553659 25/3 23 25 3 100 18 21 39 0.46153846 0.7468986 25/3 24 25 3 100 12 20 32 0.37500000 0.6590580 25/3 25 25 3 100 17 20 37 0.45945946 0.7448131 25/3 26 25 3 100 15 26 41 0.36585366 0.6495880 25/3 27 25 3 100 19 0 19 1.00000000 1.5707963 25/3 28 25 3 100 25 23 48 0.52083333 0.8062375 25/3 29 25 3 100 15 19 34 0.44117647 0.7264381 25/3 30 25 3 100 12 21 33 0.36363636 0.6472848 25/3 31 18 1 100 30 23 53 0.56603774 0.8516294 18/1 32 18 1 100 18 22 40 0.45000000 0.7353145 18/1 33 18 1 100 20 26 46 0.43478261 0.7199944 18/1 34 18 1 100 21 16 37 0.56756757 0.8531731 18/1 35 18 1 100 17 14 31 0.54838710 0.8338611 18/1 36 18 1 100 26 21 47 0.55319149 0.8386905 18/1 37 18 1 100 19 23 42 0.45238095 0.7377068 18/1 38 18 1 100 24 19 43 0.55813953 0.8436695 18/1 39 18 1 100 25 21 46 0.54347826 0.8289314 18/1 40 18 1 100 14 20 34 0.41176471 0.6966984 18/1 41 18 2 100 18 16 34 0.52941176 0.8148269 18/2 42 18 2 100 23 19 42 0.54761905 0.8330895 18/2 43 18 2 100 19 20 39 0.48717949 0.7725762 18/2 44 18 2 100 25 20 45 0.55555556 0.8410687 18/2 45 18 2 100 19 21 40 0.47500000 0.7603877 18/2 46 18 2 100 20 23 43 0.46511628 0.7504861 18/2 47 18 2 100 23 24 47 0.48936170 0.7747591 18/2 48 18 2 100 22 20 42 0.52380952 0.8092167 18/2 49 18 2 100 25 19 44 0.56818182 0.8537931 18/2 50 18 2 100 19 26 45 0.42222222 0.7073032 18/2 51 18 3 100 21 20 41 0.51219512 0.7975945 18/3 52 18 3 100 22 24 46 0.47826087 0.7636522 18/3 53 18 3 100 19 26 45 0.42222222 0.7073032 18/3 54 18 3 100 17 22 39 0.43589744 0.7211187 18/3 55 18 3 100 22 23 45 0.48888889 0.7742861 18/3 56 18 3 100 20 25 45 0.44444444 0.7297277 18/3 57 18 3 100 25 23 48 0.52083333 0.8062375 18/3 58 18 3 100 24 21 45 0.53333333 0.8187562 18/3 59 18 3 100 23 25 48 0.47916667 0.7645588 18/3 60 18 3 100 25 22 47 0.53191489 0.8173348 18/3 61 s 1 100 22 23 45 0.48888889 0.7742861 s/1 62 s 1 100 25 18 43 0.58139535 0.8671574 s/1 63 s 1 100 19 20 39 0.48717949 0.7725762 s/1 64 s 1 100 22 19 41 0.53658537 0.8220163 s/1 65 s 1 100 18 18 36 0.50000000 0.7853982 s/1 66 s 1 100 23 18 41 0.56097561 0.8465259 s/1 67 s 1 100 23 20 43 0.53488372 0.8203102 s/1 68 s 1 100 24 21 45 0.53333333 0.8187562 s/1 69 s 1 100 21 18 39 0.53846154 0.8238977 s/1 70 s 1 100 25 22 47 0.53191489 0.8173348 s/1 71 s 2 100 20 24 44 0.45454545 0.7398808 s/2 72 s 2 100 18 19 37 0.48648649 0.7718830 s/2 73 s 2 100 20 18 38 0.52631579 0.8117261 s/2 74 s 2 100 19 11 30 0.63333333 0.9203646 s/2 75 s 2 100 20 23 43 0.46511628 0.7504861 s/2 76 s 2 100 23 22 45 0.51111111 0.7965102 s/2 77 s 2 100 23 24 47 0.48936170 0.7747591 s/2 78 s 2 100 24 18 42 0.57142857 0.8570719 s/2 79 s 2 100 20 17 37 0.54054054 0.8259833 s/2 80 s 2 100 23 20 43 0.53488372 0.8203102 s/2 81 s 3 100 19 21 40 0.47500000 0.7603877 s/3 82 s 3 100 17 18 35 0.48571429 0.7711105 s/3 83 s 3 100 10 19 29 0.34482759 0.6276203 s/3 84 s 3 100 17 21 38 0.44736842 0.7326689 s/3 85 s 3 100 20 22 42 0.47619048 0.7615796 s/3 86 s 3 100 8 17 25 0.32000000 0.6012642 s/3 87 s 3 100 21 12 33 0.63636364 0.9235115 s/3 88 s 3 100 17 22 39 0.43589744 0.7211187 s/3 89 s 3 100 18 21 39 0.46153846 0.7468986 s/3 90 s 3 100 21 22 43 0.48837209 0.7737692 s/3 91 l 1 100 21 20 41 0.51219512 0.7975945 l/1 92 l 1 100 21 20 41 0.51219512 0.7975945 l/1 93 l 1 100 15 18 33 0.45454545 0.7398808 l/1 94 l 1 100 4 8 12 0.33333333 0.6154797 l/1 95 l 1 100 11 10 21 0.52380952 0.8092167 l/1 96 l 1 100 5 18 23 0.21739130 0.4850498 l/1 97 l 1 100 9 18 27 0.33333333 0.6154797 l/1 98 l 1 100 6 18 24 0.25000000 0.5235988 l/1 99 l 1 100 14 1 15 0.93333333 1.3096389 l/1 100 l 1 100 15 26 41 0.36585366 0.6495880 l/1 101 l 2 100 21 20 41 0.51219512 0.7975945 l/2 102 l 2 100 21 21 42 0.50000000 0.7853982 l/2 103 l 2 100 8 12 20 0.40000000 0.6847192 l/2 104 l 2 100 14 9 23 0.60869565 0.8949687 l/2 105 l 2 100 14 12 26 0.53846154 0.8238977 l/2 106 l 2 100 27 23 50 0.54000000 0.8254410 l/2 107 l 2 100 7 16 23 0.30434783 0.5843739 l/2 108 l 2 100 13 23 36 0.36111111 0.6446581 l/2 109 l 2 100 24 25 49 0.48979592 0.7751934 l/2 110 l 2 100 26 24 50 0.52000000 0.8054035 l/2 111 l 3 100 23 22 45 0.51111111 0.7965102 l/3 112 l 3 100 23 25 48 0.47916667 0.7645588 l/3 113 l 3 100 21 23 44 0.47727273 0.7626631 l/3 114 l 3 100 26 21 47 0.55319149 0.8386905 l/3 115 l 3 100 22 16 38 0.57894737 0.8646773 l/3 116 l 3 100 22 22 44 0.50000000 0.7853982 l/3 117 l 3 100 25 20 45 0.55555556 0.8410687 l/3 118 l 3 100 29 26 55 0.52727273 0.8126844 l/3 119 l 3 100 26 20 46 0.56521739 0.8508019 l/3 120 l 3 100 24 22 46 0.52173913 0.8071441 l/3 121 25 1 50 20 18 38 0.52631579 0.8117261 25/1 122 25 1 50 19 19 38 0.50000000 0.7853982 25/1 123 25 1 50 16 23 39 0.41025641 0.6951656 25/1 124 25 1 50 20 25 45 0.44444444 0.7297277 25/1 125 25 1 50 17 23 40 0.42500000 0.7101140 25/1 126 25 1 50 20 20 40 0.50000000 0.7853982 25/1 127 25 1 50 19 21 40 0.47500000 0.7603877 25/1 128 25 1 50 21 26 47 0.44680851 0.7321058 25/1 129 25 1 50 18 20 38 0.47368421 0.7590702 25/1 130 25 1 50 8 22 30 0.26666667 0.5426391 25/1 131 25 2 50 17 24 41 0.41463415 0.6996120 25/2 132 25 2 50 3 19 22 0.13636364 0.3782282 25/2 133 25 2 50 8 14 22 0.36363636 0.6472848 25/2 134 25 2 50 19 22 41 0.46341463 0.7487801 25/2 135 25 2 50 3 24 27 0.11111111 0.3398369 25/2 136 25 2 50 15 22 37 0.40540541 0.6902300 25/2 137 25 2 50 2 9 11 0.18181818 0.4405107 25/2 138 25 2 50 16 19 35 0.45714286 0.7424884 25/2 139 25 2 50 1 23 24 0.04166667 0.2055689 25/2 140 25 2 50 18 16 34 0.52941176 0.8148269 25/2 141 25 3 50 0 17 17 0.00000000 0.0000000 25/3 142 25 3 50 6 20 26 0.23076923 0.5010930 25/3 143 25 3 50 12 25 37 0.32432432 0.6058911 25/3 144 25 3 50 12 21 33 0.36363636 0.6472848 25/3 145 25 3 50 13 22 145 0.84827586 1.1706883 25/3 146 25 3 50 14 22 36 0.38888889 0.6733516 25/3 147 25 3 50 17 25 42 0.40476190 0.6895746 25/3 148 25 3 50 15 23 38 0.39473684 0.6793415 25/3 149 25 3 50 14 25 39 0.35897436 0.6424324 25/3 150 25 3 50 23 24 47 0.48936170 0.7747591 25/3 151 18 1 50 9 21 30 0.30000000 0.5796397 18/1 152 18 1 50 18 19 37 0.48648649 0.7718830 18/1 153 18 1 50 15 25 40 0.37500000 0.6590580 18/1 154 18 1 50 25 23 48 0.52083333 0.8062375 18/1 155 18 1 50 19 22 41 0.46341463 0.7487801 18/1 156 18 1 50 18 25 43 0.41860465 0.7036390 18/1 157 18 1 50 18 21 39 0.46153846 0.7468986 18/1 158 18 1 50 20 21 41 0.48780488 0.7732018 18/1 159 18 1 50 8 22 30 0.26666667 0.5426391 18/1 160 18 1 50 14 25 39 0.35897436 0.6424324 18/1 161 18 2 50 11 21 32 0.34375000 0.6264863 18/2 162 18 2 50 22 21 43 0.51162791 0.7970271 18/2 163 18 2 50 4 16 20 0.20000000 0.4636476 18/2 164 18 2 50 20 23 43 0.46511628 0.7504861 18/2 165 18 2 50 21 22 43 0.48837209 0.7737692 18/2 166 18 2 50 18 20 38 0.47368421 0.7590702 18/2 167 18 2 50 9 17 26 0.34615385 0.6290148 18/2 168 18 2 50 20 24 44 0.45454545 0.7398808 18/2 169 18 2 50 13 20 33 0.39393939 0.6785256 18/2 170 18 2 50 20 21 41 0.48780488 0.7732018 18/2 171 18 3 50 6 14 20 0.30000000 0.5796397 18/3 172 18 3 50 19 25 44 0.43181818 0.7170032 18/3 173 18 3 50 7 21 28 0.25000000 0.5235988 18/3 174 18 3 50 19 24 43 0.44186047 0.7271268 18/3 175 18 3 50 21 23 44 0.47727273 0.7626631 18/3 176 18 3 50 16 20 36 0.44444444 0.7297277 18/3 177 18 3 50 23 26 49 0.46938776 0.7547668 18/3 178 18 3 50 22 20 42 0.52380952 0.8092167 18/3 179 18 3 50 13 20 33 0.39393939 0.6785256 18/3 180 18 3 50 18 24 42 0.42857143 0.7137244 18/3 181 s 1 50 14 21 35 0.40000000 0.6847192 s/1 182 s 1 50 16 21 37 0.43243243 0.7176232 s/1 183 s 1 50 18 18 36 0.50000000 0.7853982 s/1 184 s 1 50 12 16 28 0.42857143 0.7137244 s/1 185 s 1 50 15 17 32 0.46875000 0.7541278 s/1 186 s 1 50 17 22 39 0.43589744 0.7211187 s/1 187 s 1 50 3 20 23 0.13043478 0.3695089 s/1 188 s 1 50 18 20 38 0.47368421 0.7590702 s/1 189 s 1 50 18 23 41 0.43902439 0.7242704 s/1 190 s 1 50 9 19 28 0.32142857 0.6027946 s/1 191 s 2 50 16 24 40 0.40000000 0.6847192 s/2 192 s 2 50 20 22 42 0.47619048 0.7615796 s/2 193 s 2 50 18 20 38 0.47368421 0.7590702 s/2 194 s 2 50 22 22 44 0.50000000 0.7853982 s/2 195 s 2 50 19 23 42 0.45238095 0.7377068 s/2 196 s 2 50 13 15 28 0.46428571 0.7496534 s/2 197 s 2 50 13 15 28 0.46428571 0.7496534 s/2 198 s 2 50 18 20 38 0.47368421 0.7590702 s/2 199 s 2 50 12 26 38 0.31578947 0.5967431 s/2 200 s 2 50 7 21 28 0.25000000 0.5235988 s/2 201 s 3 50 13 22 35 0.37142857 0.6553659 s/3 202 s 3 50 16 21 37 0.43243243 0.7176232 s/3 203 s 3 50 12 17 29 0.41379310 0.6987583 s/3 204 s 3 50 17 10 27 0.62962963 0.9165257 s/3 205 s 3 50 7 18 25 0.28000000 0.5575988 s/3 206 s 3 50 7 9 16 0.43750000 0.7227342 s/3 207 s 3 50 8 20 28 0.28571429 0.5639426 s/3 208 s 3 50 5 15 20 0.25000000 0.5235988 s/3 209 s 3 50 9 20 29 0.31034483 0.5908728 s/3 210 s 3 50 6 15 21 0.28571429 0.5639426 s/3 211 l 1 50 4 18 22 0.18181818 0.4405107 l/1 212 l 1 50 7 16 23 0.30434783 0.5843739 l/1 213 l 1 50 4 20 24 0.16666667 0.4205343 l/1 214 l 1 50 21 24 45 0.46666667 0.7520401 l/1 215 l 1 50 7 24 31 0.22580645 0.4951811 l/1 216 l 1 50 9 19 28 0.32142857 0.6027946 l/1 217 l 1 50 2 13 15 0.13333333 0.3737922 l/1 218 l 1 50 5 24 29 0.17241379 0.4281928 l/1 219 l 1 50 23 21 44 0.52272727 0.8081333 l/1 220 l 1 50 16 19 35 0.45714286 0.7424884 l/1 221 l 2 50 20 16 36 0.55555556 0.8410687 l/2 222 l 2 50 12 8 20 0.60000000 0.8860771 l/2 223 l 2 50 15 23 38 0.39473684 0.6793415 l/2 224 l 2 50 3 18 21 0.14285714 0.3875967 l/2 225 l 2 50 8 16 24 0.33333333 0.6154797 l/2 226 l 2 50 9 19 28 0.32142857 0.6027946 l/2 227 l 2 50 22 22 44 0.50000000 0.7853982 l/2 228 l 2 50 9 10 19 0.47368421 0.7590702 l/2 229 l 2 50 13 23 36 0.36111111 0.6446581 l/2 230 l 2 50 15 20 35 0.42857143 0.7137244 l/2 231 l 3 50 20 21 41 0.48780488 0.7732018 l/3 232 l 3 50 9 18 27 0.33333333 0.6154797 l/3 233 l 3 50 18 18 36 0.50000000 0.7853982 l/3 234 l 3 50 9 16 25 0.36000000 0.6435011 l/3 235 l 3 50 22 26 48 0.45833333 0.7436831 l/3 236 l 3 50 21 17 38 0.55263158 0.8381274 l/3 237 l 3 50 19 23 42 0.45238095 0.7377068 l/3 238 l 3 50 19 20 39 0.48717949 0.7725762 l/3 239 l 3 50 18 21 39 0.46153846 0.7468986 l/3 240 l 3 50 21 22 43 0.48837209 0.7737692 l/3 241 25 1 25 19 23 42 0.45238095 0.7377068 25/1 242 25 1 25 0 7 7 0.00000000 0.0000000 25/1 243 25 1 25 14 9 23 0.60869565 0.8949687 25/1 244 25 1 25 0 14 14 0.00000000 0.0000000 25/1 245 25 1 25 14 22 36 0.38888889 0.6733516 25/1 246 25 1 25 0 3 3 0.00000000 0.0000000 25/1 247 25 1 25 15 23 38 0.39473684 0.6793415 25/1 248 25 1 25 14 20 34 0.41176471 0.6966984 25/1 249 25 1 25 7 13 20 0.35000000 0.6330518 25/1 250 25 1 25 15 20 35 0.42857143 0.7137244 25/1 251 25 2 25 0 9 9 0.00000000 0.0000000 25/2 252 25 2 25 16 23 39 0.41025641 0.6951656 25/2 253 25 2 25 15 25 40 0.37500000 0.6590580 25/2 254 25 2 25 17 19 36 0.47222222 0.7576061 25/2 255 25 2 25 1 10 11 0.09090909 0.3062774 25/2 256 25 2 25 2 20 22 0.09090909 0.3062774 25/2 257 25 2 25 7 15 22 0.31818182 0.5993139 25/2 258 25 2 25 1 18 19 0.05263158 0.2314774 25/2 259 25 2 25 3 22 25 0.12000000 0.3537416 25/2 260 25 2 25 9 21 30 0.30000000 0.5796397 25/2 261 25 3 25 2 23 25 0.08000000 0.2867566 25/3 262 25 3 25 1 19 20 0.05000000 0.2255134 25/3 263 25 3 25 8 21 29 0.27586207 0.5529804 25/3 264 25 3 25 10 20 30 0.33333333 0.6154797 25/3 265 25 3 25 6 6 12 0.50000000 0.7853982 25/3 266 25 3 25 0 15 15 0.00000000 0.0000000 25/3 267 25 3 25 1 17 18 0.05555556 0.2379411 25/3 268 25 3 25 3 24 27 0.11111111 0.3398369 25/3 269 25 3 25 7 19 26 0.26923077 0.5455338 25/3 270 25 3 25 4 22 26 0.15384615 0.4030571 25/3 271 18 1 25 6 18 24 0.25000000 0.5235988 18/1 272 18 1 25 0 14 14 0.00000000 0.0000000 18/1 273 18 1 25 7 19 26 0.26923077 0.5455338 18/1 274 18 1 25 5 22 27 0.18518519 0.4448600 18/1 275 18 1 25 3 10 13 0.23076923 0.5010930 18/1 276 18 1 25 14 24 38 0.36842105 0.6522512 18/1 277 18 1 25 12 21 33 0.36363636 0.6472848 18/1 278 18 1 25 0 23 23 0.00000000 0.0000000 18/1 279 18 1 25 14 17 31 0.45161290 0.7369352 18/1 280 18 1 25 2 12 14 0.14285714 0.3875967 18/1 281 18 2 25 8 19 27 0.29629630 0.5755915 18/2 282 18 2 25 12 20 32 0.37500000 0.6590580 18/2 283 18 2 25 10 18 28 0.35714286 0.6405223 18/2 284 18 2 25 0 6 6 0.00000000 0.0000000 18/2 285 18 2 25 8 16 24 0.33333333 0.6154797 18/2 286 18 2 25 8 21 29 0.27586207 0.5529804 18/2 287 18 2 25 2 18 20 0.10000000 0.3217506 18/2 288 18 2 25 5 17 22 0.22727273 0.4969325 18/2 289 18 2 25 3 20 23 0.13043478 0.3695089 18/2 290 18 2 25 7 17 24 0.29166667 0.5705104 18/2 291 18 3 25 11 20 31 0.35483871 0.6381162 18/3 292 18 3 25 8 19 27 0.29629630 0.5755915 18/3 293 18 3 25 6 14 20 0.30000000 0.5796397 18/3 294 18 3 25 19 19 38 0.50000000 0.7853982 18/3 295 18 3 25 8 21 29 0.27586207 0.5529804 18/3 296 18 3 25 3 21 24 0.12500000 0.3613671 18/3 297 18 3 25 4 22 26 0.15384615 0.4030571 18/3 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0.20833333 0.4739849 s/2 321 s 3 25 11 18 29 0.37931034 0.6635047 s/3 322 s 3 25 12 16 28 0.42857143 0.7137244 s/3 323 s 3 25 2 15 17 0.11764706 0.3501058 s/3 324 s 3 25 12 16 28 0.42857143 0.7137244 s/3 325 s 3 25 13 20 33 0.39393939 0.6785256 s/3 326 s 3 25 9 23 32 0.28125000 0.5589899 s/3 327 s 3 25 2 18 20 0.10000000 0.3217506 s/3 328 s 3 25 0 11 11 0.00000000 0.0000000 s/3 329 s 3 25 1 5 6 0.16666667 0.4205343 s/3 330 s 3 25 6 19 25 0.24000000 0.5119727 s/3 331 l 1 25 1 16 17 0.05882353 0.2449787 l/1 332 l 1 25 16 17 33 0.48484848 0.7702443 l/1 333 l 1 25 1 14 15 0.06666667 0.2611574 l/1 334 l 1 25 4 21 25 0.16000000 0.4115168 l/1 335 l 1 25 5 20 25 0.20000000 0.4636476 l/1 336 l 1 25 4 20 24 0.16666667 0.4205343 l/1 337 l 1 25 4 14 18 0.22222222 0.4908827 l/1 338 l 1 25 1 15 16 0.06250000 0.2526803 l/1 339 l 1 25 12 22 34 0.35294118 0.6361321 l/1 340 l 1 25 4 20 24 0.16666667 0.4205343 l/1 341 l 2 25 19 24 43 0.44186047 0.7271268 l/2 342 l 2 25 4 22 26 0.15384615 0.4030571 l/2 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s/2 432 s 2 10 8 1 9 0.88888889 1.2309594 s/2 433 s 2 10 3 22 25 0.12000000 0.3537416 s/2 434 s 2 10 5 21 26 0.19230769 0.4539613 s/2 435 s 2 10 6 4 10 0.60000000 0.8860771 s/2 436 s 2 10 6 11 17 0.35294118 0.6361321 s/2 437 s 3 10 3 4 7 0.42857143 0.7137244 s/3 438 s 3 10 5 14 19 0.26315789 0.5386635 s/3 439 s 3 10 10 4 14 0.71428571 1.0068537 s/3 440 s 3 10 3 16 19 0.15789474 0.4086379 s/3 441 s 3 10 5 14 19 0.26315789 0.5386635 s/3 442 s 3 10 14 18 32 0.43750000 0.7227342 s/3 443 s 3 10 0 6 6 0.00000000 0.0000000 s/3 444 s 3 10 10 16 26 0.38461538 0.6689641 s/3 445 s 3 10 7 9 16 0.43750000 0.7227342 s/3 446 l 1 10 0 2 2 0.00000000 0.0000000 l/1 447 l 1 10 0 4 4 0.00000000 0.0000000 l/1 448 l 1 10 2 19 21 0.09523810 0.3137279 l/1 449 l 1 10 2 14 16 0.12500000 0.3613671 l/1 450 l 1 10 0 17 17 0.00000000 0.0000000 l/1 451 l 1 10 9 13 22 0.40909091 0.6939806 l/1 452 l 1 10 4 8 12 0.33333333 0.6154797 l/1 453 l 1 10 3 13 16 0.18750000 0.4478324 l/1 454 l 1 10 10 16 26 0.38461538 0.6689641 l/1 455 l 1 10 3 11 14 0.21428571 0.4812754 l/1 456 l 2 10 6 7 13 0.46153846 0.7468986 l/2 457 l 2 10 1 11 12 0.08333333 0.2928428 l/2 458 l 2 10 1 15 16 0.06250000 0.2526803 l/2 459 l 2 10 2 17 19 0.10526316 0.3304226 l/2 460 l 2 10 2 15 17 0.11764706 0.3501058 l/2 461 l 2 10 2 2 4 0.50000000 0.7853982 l/2 462 l 2 10 5 14 19 0.26315789 0.5386635 l/2 463 l 2 10 17 14 31 0.54838710 0.8338611 l/2 464 l 2 10 10 11 21 0.47619048 0.7615796 l/2 465 l 2 10 9 14 23 0.39130435 0.6758276 l/2 466 l 3 10 4 5 9 0.44444444 0.7297277 l/3 467 l 3 10 1 3 4 0.25000000 0.5235988 l/3 468 l 3 10 13 9 22 0.59090909 0.8768157 l/3 469 l 3 10 3 20 23 0.13043478 0.3695089 l/3 470 l 3 10 12 13 25 0.48000000 0.7653928 l/3 471 l 3 10 0 7 7 0.00000000 0.0000000 l/3 472 l 3 10 6 7 13 0.46153846 0.7468986 l/3 473 l 3 10 10 6 16 0.62500000 0.9117383 l/3 474 l 3 10 1 1 2 0.50000000 0.7853982 l/3 475 l 3 10 3 10 13 0.23076923 0.5010930 l/3 ======================== Federico C.F. Calboli Department of Biology University College London Room 327 Darwin Building Gower Street London WClE 6BT Tel: (+44) 020 7679 4395 Fax (+44) 020 7679 7096 f.calboli at ucl.ac.uk
Federico - I'm coming to this from outside the field, and I hope Doug Bates will reply ... but I would question the use of normal theory linear models with counted data. Why not logistic regression (binomial) or log-linear models (Poisson) ? You see, coming to the question from outside, I'm still back at the point of needing to answer *that* question for myself, before I can think about the random-effects aspects of the problem. I don't yet understand "vials within cages". Are the vials open or closed ? What determines the total number per vial ? (Thus, is a binomial or a Poisson error model appropriate ?) And, what is "temperature" in the Bartlett test, and why does it make sense to *cross* "cage" with "temperature" ? Was every cage in fact tested at multiple temperatures ? (I would guess not, but I don't fully understand the experimental setup.) So ... in the end ... I offer you many questions and *zero* answers ! - tom blackwell - u michigan medical school - ann arbor - On Tue, 13 May 2003, Federico Calboli wrote:> I would like to ask a couple of questions on a LME model. > > I tested 4 selection lines at 4 food concentrations against a standard > competitor stock. I had 3 replicate cages per selection line. In each cage > I have 10 vials. I counted the number of wild type flies and competitor > stock emerging in each vial. My main question is: is there any difference > between selection lines? > > I did fit the following model: > > mod1<-lme(wt~selection*food, random=~1|c1/food, competition) > > The quantile plot is straight, the plot of residuals looks good, the > standardized residual plot seems ok... BUT if I do a bartlett test for > homogeneity of variance (done by cage*temperature, 48 cages in all) the > variance is NOT homogeneous. Is my model still accettable? if not, what > could I do? > > The same model on asin(sqrt(wild type/total)) does not fit anywhere as well. > > my dataset (NB *wt* is the number of wild type flies in each vial; *spa* is > the number of comepetitor stock flies in each vial, *p1* is > asin(sqrt(competition$prop)), *c1* is the cage nested in selection using > getGroups...): > > selection cage food wt spa tot prop p1 c1 > > (475 lines of data deleted) > > Federico C.F. Calboli > > Department of Biology > University College London > Room 327 > Darwin Building > Gower Street > London > WClE 6BT > > Tel: (+44) 020 7679 4395 > Fax (+44) 020 7679 7096 > f.calboli at ucl.ac.uk