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R version 3.4.3 Patched (2018-02-11 r74243) -- "Kite-Eating Tree"Copyright (C) 2018 The R Foundation for Statistical ComputingPlatform: x86_64-apple-darwin17.4.0 (64-bit)R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> library(nlme)>> op <- options(digits = 3) # reduce rounding differences>> Ovary[c(1,272), 2] <- NA> fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,+ correlation = corAR1(form = ~ 1 | Mare), na.action=na.exclude)> fitted(fm1)1 2 3 4 5 6 7 8 9 10 11 12 13NA 12.86 12.06 11.27 10.55 9.96 9.54 9.34 9.36 9.60 10.05 10.67 11.4114 15 16 17 18 19 20 21 22 23 24 25 2612.21 13.00 13.71 14.31 14.72 14.93 14.91 14.66 14.21 13.59 12.86 12.06 11.2727 28 29 30 31 32 33 34 35 36 37 38 3910.55 9.96 9.54 13.79 13.01 12.14 11.27 10.49 9.86 9.46 9.32 9.45 9.8540 41 42 43 44 45 46 47 48 49 50 51 5210.47 11.26 12.13 13.00 13.78 14.41 14.81 14.95 14.81 14.41 13.79 13.01 12.1453 54 55 56 57 58 59 60 61 62 63 64 6511.27 10.49 9.86 9.46 13.90 13.10 12.19 11.27 10.45 9.81 9.42 9.32 9.5366 67 68 69 70 71 72 73 74 75 76 77 7810.03 10.75 11.62 12.54 13.42 14.17 14.69 14.93 14.87 14.52 13.90 13.10 12.1979 80 81 82 83 84 85 86 87 88 89 90 9111.27 10.45 9.81 9.42 13.59 12.86 12.06 11.27 10.55 9.96 9.54 9.34 9.3692 93 94 95 96 97 98 99 100 101 102 103 1049.60 10.05 10.67 11.41 12.21 13.00 13.71 14.31 14.72 14.93 14.91 14.66 14.21105 106 107 108 109 110 111 112 113 114 115 116 11713.59 12.86 12.06 11.27 10.55 9.96 9.54 13.59 12.86 12.06 11.27 10.55 9.96118 119 120 121 122 123 124 125 126 127 128 129 1309.54 9.34 9.36 9.60 10.05 10.67 11.41 12.21 13.00 13.71 14.31 14.72 14.93131 132 133 134 135 136 137 138 139 140 141 142 14314.91 14.66 14.21 13.59 12.86 12.06 11.27 10.55 9.96 9.54 13.59 12.86 12.06144 145 146 147 148 149 150 151 152 153 154 155 15611.27 10.55 9.96 9.54 9.34 9.36 9.60 10.05 10.67 11.41 12.21 13.00 13.71157 158 159 160 161 162 163 164 165 166 167 168 16914.31 14.72 14.93 14.91 14.66 14.21 13.59 12.86 12.06 11.27 10.55 9.96 9.54170 171 172 173 174 175 176 177 178 179 180 181 18213.79 13.01 12.14 11.27 10.49 9.86 9.46 9.32 9.45 9.85 10.47 11.26 12.13183 184 185 186 187 188 189 190 191 192 193 194 19513.00 13.78 14.41 14.81 14.95 14.81 14.41 13.79 13.01 12.14 11.27 10.49 9.86196 197 198 199 200 201 202 203 204 205 206 207 2089.46 13.42 12.73 11.99 11.27 10.61 10.05 9.63 9.38 9.32 9.45 9.77 10.24209 210 211 212 213 214 215 216 217 218 219 220 22110.85 11.54 12.27 13.00 13.66 14.22 14.64 14.88 14.94 14.81 14.50 14.02 13.42222 223 224 225 226 227 228 229 230 231 232 233 23412.73 11.99 11.27 10.61 10.05 9.63 14.02 13.19 12.24 11.27 10.41 9.75 9.38235 236 237 238 239 240 241 242 243 244 245 246 2479.35 9.64 10.24 11.07 12.03 13.00 13.86 14.52 14.88 14.92 14.62 14.02 13.19248 249 250 251 252 253 254 255 256 257 258 259 26012.24 11.27 10.41 9.75 9.38 13.59 12.86 12.06 11.27 10.55 9.96 9.54 9.34261 262 263 264 265 266 267 268 269 270 271 272 2739.36 9.60 10.05 10.67 11.41 12.21 13.00 13.71 14.31 14.72 14.93 NA 14.66274 275 276 277 278 279 280 281 282 283 284 285 28614.21 13.59 12.86 12.06 11.27 10.55 9.96 9.54 13.79 13.01 12.14 11.27 10.49287 288 289 290 291 292 293 294 295 296 297 298 2999.86 9.46 9.32 9.45 9.85 10.47 11.26 12.13 13.00 13.78 14.41 14.81 14.95300 301 302 303 304 305 306 307 30814.81 14.41 13.79 13.01 12.14 11.27 10.49 9.86 9.46attr(,"label")[1] "Fitted values"> residuals(fm1)1 2 3 4 5 6 7 8NA 2.1439 6.9394 4.7290 2.4488 0.0405 2.4560 4.66189 10 11 12 13 14 15 163.6412 10.3959 11.9456 4.3270 6.5900 4.7945 1.0049 4.285117 18 19 20 21 22 23 24-0.3066 1.2779 2.0720 3.0927 3.3380 2.7883 0.4069 -0.856125 26 27 28 29 30 31 32-0.0606 2.7290 -0.5512 1.0405 6.4560 -7.7936 -7.0102 -4.141033 34 35 36 37 38 39 40-4.2710 5.5146 0.1390 3.5409 -0.3189 -2.4542 -3.8517 -2.472541 42 43 44 45 46 47 48-3.2559 -6.1251 -4.9951 -6.7808 -5.4051 -8.8070 -10.9472 -9.811949 50 51 52 53 54 55 56-6.4144 -2.7936 -0.0102 -2.1410 -5.2710 -3.4854 -3.8610 -4.459157 58 59 60 61 62 63 64-0.9042 -2.0982 -2.1875 -5.2710 -2.4479 -3.8074 -0.4189 -0.324565 66 67 68 69 70 71 720.4655 -2.0261 3.2540 1.3838 1.4576 2.5757 5.8338 6.312273 74 75 76 77 78 79 8010.0674 8.1260 4.4817 8.0958 2.9018 8.8125 7.7290 9.552181 82 83 84 85 86 87 887.1926 14.5811 -4.5931 -3.8561 -5.0606 -5.2710 -3.5512 -3.959589 90 91 92 93 94 95 96-8.5440 -8.3382 -8.3588 -4.6041 -4.0544 -7.6730 -6.4100 -9.205597 98 99 100 101 102 103 104-6.9951 -5.7149 -8.3066 -9.7221 -8.9280 -6.9073 -3.6620 -0.2117105 106 107 108 109 110 111 112-5.5931 -3.8561 -2.0606 -4.2710 -3.5512 -3.9595 1.4560 -3.5931113 114 115 116 117 118 119 120-0.8561 -0.0606 5.7290 -1.5512 0.0405 -6.5440 2.6618 3.6412121 122 123 124 125 126 127 128-0.6041 -6.0544 -3.6730 -7.4100 -0.2055 1.0049 -1.7149 0.6934129 130 131 132 133 134 135 1362.2779 0.0720 -1.9073 3.3380 4.7883 -0.5931 -3.8561 -0.0606137 138 139 140 141 142 143 144-3.2710 -0.5512 -4.9595 4.4560 2.4069 4.1439 0.9394 5.7290145 146 147 148 149 150 151 1524.4488 -0.9595 -1.5440 -4.3382 -0.3588 -1.6041 -2.0544 2.3270153 154 155 156 157 158 159 1602.5900 0.7945 1.0049 0.2851 -3.3066 2.2779 6.0720 6.0927161 162 163 164 165 166 167 1686.3380 5.7883 3.4069 5.1439 9.9394 -1.2710 0.4488 1.0405169 170 171 172 173 174 175 1762.4560 4.2064 -0.0102 1.8590 0.7290 0.5146 -1.8610 -4.4591177 178 179 180 181 182 183 184-1.3189 0.5458 1.1483 -0.4725 0.7441 -2.1251 -3.9951 -1.7808185 186 187 188 189 190 191 192-0.4051 1.1930 -1.9472 -3.8119 -1.4144 -0.7936 -2.0102 -1.1410193 194 195 196 197 198 199 200-3.2710 3.5146 -5.8610 -2.4591 -0.4177 -3.7259 3.0063 3.7290201 202 203 204 205 206 207 2081.3930 -2.0471 0.3708 -3.3821 -0.3224 -1.4542 0.2314 -4.2441209 210 211 212 213 214 215 216-2.8484 1.4598 -0.2724 -0.9951 1.3409 6.7809 10.3631 6.1159217 218 219 220 221 222 223 2246.0562 9.1881 5.5025 5.9780 4.5823 7.2741 8.0063 7.7290225 226 227 228 229 230 231 2321.3930 -3.0471 -1.6292 -4.0220 0.8054 -0.2392 -1.2710 -3.4068233 234 235 236 237 238 239 2402.2493 0.6179 -1.3452 0.3554 4.7559 3.9285 -0.0269 6.0049241 242 243 244 245 246 247 2481.1406 1.4846 0.1159 2.0791 -0.6215 1.9780 1.8054 -1.2392249 250 251 252 253 254 255 256-1.2710 -3.4067 -5.7507 -1.3821 -2.5931 3.1439 2.9394 0.7290257 258 259 260 261 262 263 2640.4488 -3.9595 1.4560 2.6618 1.6412 6.3959 4.9456 0.3270265 266 267 268 269 270 271 272-4.4100 1.7945 7.0049 8.2851 8.6934 6.2779 6.0720 NA273 274 275 276 277 278 279 2807.3380 7.7883 3.4069 4.1439 4.9394 5.7290 3.4488 2.0405281 282 283 284 285 286 287 2881.4560 -4.7936 -5.0102 -4.1410 -3.2710 -2.4854 -3.8610 -2.4591289 290 291 292 293 294 295 296-1.3189 0.5458 0.1483 3.5275 1.7441 -4.1251 -4.9951 -5.7808297 298 299 300 301 302 303 304-5.4051 1.1930 -2.9472 -4.8119 -2.4144 -1.7936 -4.0102 -6.1410305 306 307 308-2.2710 -3.4854 -4.8610 -4.4591attr(,"std")[1] NA 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[16] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[31] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[46] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[61] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[76] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[91] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[106] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[121] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[136] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[151] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[166] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[181] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[196] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[211] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[226] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[241] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[256] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[271] 4.58 NA 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[286] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58[301] 4.58 4.58 4.58 4.58 4.58 4.58 4.58 4.58attr(,"label")[1] "Residuals"> summary(fm1)Generalized least squares fit by REMLModel: follicles ~ sin(2 * pi * Time) + cos(2 * pi * Time)Data: OvaryAIC BIC logLik1560 1579 -775Correlation Structure: AR(1)Formula: ~1 | MareParameter estimate(s):Phi0.75Coefficients:Value Std.Error t-value p-value(Intercept) 12.13 0.657 18.46 0.000sin(2 * pi * Time) -2.68 0.644 -4.16 0.000cos(2 * pi * Time) -0.86 0.690 -1.25 0.213Correlation:(Intr) s(*p*Tsin(2 * pi * Time) -0.007cos(2 * pi * Time) -0.295 0.003Standardized residuals:Min Q1 Med Q3 Max-2.3897 -0.7565 -0.0132 0.6396 3.1830Residual standard error: 4.58Degrees of freedom: 306 total; 303 residual>> Orthodont[100:102, 2] <- NA> fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1,+ na.action=na.exclude)> fitted(fm2, 0:1)fixed Subject1 23.0 25.42 24.3 26.73 25.6 28.04 27.0 29.45 23.0 21.66 24.3 22.97 25.6 24.38 27.0 25.69 23.0 22.310 24.3 23.711 25.6 25.012 27.0 26.413 23.0 24.414 24.3 25.715 25.6 27.116 27.0 28.417 23.0 21.318 24.3 22.619 25.6 23.920 27.0 25.321 23.0 24.222 24.3 25.523 25.6 26.924 27.0 28.225 23.0 21.926 24.3 23.227 25.6 24.628 27.0 25.929 23.0 22.030 24.3 23.431 25.6 24.732 27.0 26.033 23.0 23.134 24.3 24.435 25.6 25.836 27.0 27.137 23.0 26.938 24.3 28.239 25.6 29.540 27.0 30.941 23.0 21.842 24.3 23.143 25.6 24.544 27.0 25.845 23.0 22.346 24.3 23.747 25.6 25.048 27.0 26.449 23.0 22.350 24.3 23.751 25.6 25.052 27.0 26.453 23.0 22.954 24.3 24.255 25.6 25.656 27.0 26.957 23.0 23.758 24.3 25.159 25.6 26.460 27.0 27.861 23.0 21.362 24.3 22.663 25.6 23.964 27.0 25.365 20.7 19.566 22.0 20.967 23.4 22.268 24.7 23.669 20.7 20.970 22.0 22.371 23.4 23.672 24.7 25.073 20.7 21.674 22.0 22.975 23.4 24.376 24.7 25.677 20.7 22.678 22.0 23.979 23.4 25.280 24.7 26.681 20.7 20.682 22.0 22.083 23.4 23.384 24.7 24.685 20.7 19.386 22.0 20.787 23.4 22.088 24.7 23.489 20.7 20.990 22.0 22.391 23.4 23.692 24.7 25.093 20.7 21.394 22.0 22.695 23.4 24.096 24.7 25.397 20.7 19.898 22.0 21.299 23.4 22.5100 NA NA101 NA NA102 NA NA103 23.4 19.7104 24.7 21.1105 20.7 23.9106 22.0 25.2107 23.4 26.5108 24.7 27.9> fitted(fm2)M01 M01 M01 M01 M02 M02 M02 M02 M03 M03 M03 M03 M04 M04 M04 M0425.4 26.7 28.0 29.4 21.6 22.9 24.3 25.6 22.3 23.7 25.0 26.4 24.4 25.7 27.1 28.4M05 M05 M05 M05 M06 M06 M06 M06 M07 M07 M07 M07 M08 M08 M08 M0821.3 22.6 23.9 25.3 24.2 25.5 26.9 28.2 21.9 23.2 24.6 25.9 22.0 23.4 24.7 26.0M09 M09 M09 M09 M10 M10 M10 M10 M11 M11 M11 M11 M12 M12 M12 M1223.1 24.4 25.8 27.1 26.9 28.2 29.5 30.9 21.8 23.1 24.5 25.8 22.3 23.7 25.0 26.4M13 M13 M13 M13 M14 M14 M14 M14 M15 M15 M15 M15 M16 M16 M16 M1622.3 23.7 25.0 26.4 22.9 24.2 25.6 26.9 23.7 25.1 26.4 27.8 21.3 22.6 23.9 25.3F01 F01 F01 F01 F02 F02 F02 F02 F03 F03 F03 F03 F04 F04 F04 F0419.5 20.9 22.2 23.6 20.9 22.3 23.6 25.0 21.6 22.9 24.3 25.6 22.6 23.9 25.2 26.6F05 F05 F05 F05 F06 F06 F06 F06 F07 F07 F07 F07 F08 F08 F08 F0820.6 22.0 23.3 24.6 19.3 20.7 22.0 23.4 20.9 22.3 23.6 25.0 21.3 22.6 24.0 25.3F09 F09 F09 <NA> <NA> <NA> F10 F10 F11 F11 F11 F1119.8 21.2 22.5 NA NA NA 19.7 21.1 23.9 25.2 26.5 27.9attr(,"label")[1] "Fitted values (mm)"> residuals(fm2, 0:1)fixed Subject1 3.0453 0.648272 0.7026 -1.694433 3.3599 0.962864 4.0172 1.620165 -1.4547 -0.081116 -1.7974 -0.423827 -2.6401 -1.266528 -0.4828 0.890789 0.0453 0.6647610 -1.7974 -1.1779411 -1.6401 -1.0206412 0.5172 1.1366513 2.5453 1.1178614 3.2026 1.7751515 0.8599 -0.5675516 0.0172 -1.4102517 -2.9547 -1.2579218 -0.7974 0.8993819 -3.1401 -1.4433220 -0.9828 0.7139721 1.5453 0.3333222 1.2026 -0.0093823 1.3599 0.1479124 1.5172 0.3052125 -0.9547 0.0956926 -2.2974 -1.2470127 -1.1401 -0.0897228 -0.4828 0.5675829 1.0453 1.9879630 -2.7974 -1.8547431 -1.1401 -0.1974532 -1.4828 -0.5401533 0.0453 -0.0893634 -3.7974 -3.9320635 5.3599 5.2252336 -0.9828 -1.1174737 4.5453 0.6400238 3.7026 -0.2026839 5.3599 1.4546140 4.5172 0.6119141 0.0453 1.2034242 -1.2974 -0.1392843 -2.1401 -0.9819844 -1.9828 -0.8246945 -1.4547 -0.8352446 -0.7974 -0.1779447 -1.6401 -1.0206448 1.0172 1.6366549 -5.9547 -5.3352450 0.2026 0.8220651 0.3599 0.9793652 2.5172 3.1366553 -0.4547 -0.3739054 1.2026 1.2834055 -0.1401 -0.0593056 -0.9828 -0.9020157 0.0453 -0.7357558 0.2026 -0.5784659 0.3599 -0.4211660 3.0172 2.2361461 -0.9547 0.7420862 -2.7974 -1.1006263 -2.1401 -0.4433264 -1.9828 -0.2860365 0.3135 1.4559466 -2.0292 -0.8867667 -1.8719 -0.7294768 -1.7146 -0.5721769 0.3135 0.0554370 -0.5292 -0.7872871 0.6281 0.3700272 0.7854 0.5273273 -0.1865 -1.0909774 1.9708 1.0663375 1.1281 0.2236376 1.2854 0.3809277 2.8135 0.9394578 2.4708 0.5967479 1.6281 -0.2459680 1.7854 -0.0886681 0.8135 0.8786282 0.9708 1.0359283 -0.8719 -0.8067884 -1.2146 -1.1494985 -0.6865 0.6714186 -1.0292 0.3287087 -2.3719 -1.0140088 -2.2146 -0.8567089 0.8135 0.5554390 0.4708 0.2127291 -0.3719 -0.6299892 0.2854 0.0273293 2.3135 1.7322394 0.9708 0.3895395 0.1281 -0.4531896 -0.7146 -1.2958897 -0.6865 0.1614898 -1.0292 -0.1812299 -1.3719 -0.52392100 NA NA101 NA NA102 NA NA103 -4.3719 -0.74222104 -5.2146 -1.58492105 3.8135 0.64666106 2.9708 -0.19604107 4.6281 1.46126108 3.2854 0.11855> round(residuals(fm2), 2)M01 M01 M01 M01 M02 M02 M02 M02 M03 M03 M03 M03 M040.65 -1.69 0.96 1.62 -0.08 -0.42 -1.27 0.89 0.66 -1.18 -1.02 1.14 1.12M04 M04 M04 M05 M05 M05 M05 M06 M06 M06 M06 M07 M071.78 -0.57 -1.41 -1.26 0.90 -1.44 0.71 0.33 -0.01 0.15 0.31 0.10 -1.25M07 M07 M08 M08 M08 M08 M09 M09 M09 M09 M10 M10 M10-0.09 0.57 1.99 -1.85 -0.20 -0.54 -0.09 -3.93 5.23 -1.12 0.64 -0.20 1.45M10 M11 M11 M11 M11 M12 M12 M12 M12 M13 M13 M13 M130.61 1.20 -0.14 -0.98 -0.82 -0.84 -0.18 -1.02 1.64 -5.34 0.82 0.98 3.14M14 M14 M14 M14 M15 M15 M15 M15 M16 M16 M16 M16 F01-0.37 1.28 -0.06 -0.90 -0.74 -0.58 -0.42 2.24 0.74 -1.10 -0.44 -0.29 1.46F01 F01 F01 F02 F02 F02 F02 F03 F03 F03 F03 F04 F04-0.89 -0.73 -0.57 0.06 -0.79 0.37 0.53 -1.09 1.07 0.22 0.38 0.94 0.60F04 F04 F05 F05 F05 F05 F06 F06 F06 F06 F07 F07 F07-0.25 -0.09 0.88 1.04 -0.81 -1.15 0.67 0.33 -1.01 -0.86 0.56 0.21 -0.63F07 F08 F08 F08 F08 F09 F09 F09 <NA> <NA> <NA> F10 F100.03 1.73 0.39 -0.45 -1.30 0.16 -0.18 -0.52 NA NA NA -0.74 -1.58F11 F11 F11 F110.65 -0.20 1.46 0.12attr(,"label")[1] "Residuals (mm)"> summary(fm2)Linear mixed-effects model fit by REMLData: OrthodontAIC BIC logLik437 450 -213Random effects:Formula: ~1 | Subject(Intercept) ResidualStdDev: 1.8 1.44Fixed effects: distance ~ age + SexValue Std.Error DF t-value p-value(Intercept) 17.58 0.850 77 20.68 0.0000age 0.67 0.064 77 10.56 0.0000SexFemale -2.27 0.762 25 -2.98 0.0064Correlation:(Intr) ageage -0.822SexFemale -0.357 -0.006Standardized Within-Group Residuals:Min Q1 Med Q3 Max-3.7079 -0.5471 -0.0564 0.4666 3.6314Number of Observations: 105Number of Groups: 27>> Soybean[1:5, "Time"] <- NA> fm3 <- gnls(weight ~ SSlogis(Time, Asym, xmid, scal), Soybean,+ weights = varPower(), na.action=na.exclude)> fitted(fm3)1 2 3 4 5 6 7 8 9 10 11NA NA NA NA NA 7.047 10.958 14.082 15.894 16.756 0.12012 13 14 15 16 17 18 19 20 21 220.298 0.726 1.708 3.724 7.047 10.958 15.894 16.756 0.120 0.298 0.72623 24 25 26 27 28 29 30 31 32 331.708 3.724 7.047 10.958 14.082 15.894 16.756 0.120 0.298 0.726 1.70834 35 36 37 38 39 40 41 42 43 443.724 7.047 10.958 14.082 15.894 16.756 0.120 0.298 0.726 1.708 3.72445 46 47 48 49 50 51 52 53 54 557.047 10.958 15.894 0.120 0.298 0.726 1.708 3.724 7.047 10.958 14.08256 57 58 59 60 61 62 63 64 65 6615.894 16.756 0.120 0.298 0.726 1.708 3.724 7.047 10.958 15.894 16.75667 68 69 70 71 72 73 74 75 76 770.120 0.298 0.726 1.708 3.724 7.047 10.958 14.082 15.894 16.756 0.12078 79 80 81 82 83 84 85 86 87 880.298 0.726 1.708 3.724 7.047 10.958 14.082 15.894 16.756 0.120 0.29889 90 91 92 93 94 95 96 97 98 990.726 1.708 3.724 7.047 10.958 14.082 15.894 16.756 0.120 0.298 0.726100 101 102 103 104 105 106 107 108 109 1101.708 3.724 7.047 10.958 14.082 15.894 16.756 0.120 0.298 0.726 1.708111 112 113 114 115 116 117 118 119 120 1213.724 7.047 10.958 14.082 15.894 16.756 0.120 0.298 0.726 1.708 3.724122 123 124 125 126 127 128 129 130 131 1327.047 10.958 14.082 15.894 16.756 0.120 0.298 0.726 1.708 3.724 7.047133 134 135 136 137 138 139 140 141 142 14310.958 14.082 15.894 16.756 0.120 0.298 0.726 1.708 3.724 7.047 10.958144 145 146 147 148 149 150 151 152 153 15414.082 15.894 16.756 0.120 0.298 0.726 1.708 3.724 7.047 10.958 14.082155 156 157 158 159 160 161 162 163 164 16515.894 16.756 0.120 0.262 0.640 1.517 3.355 10.419 15.706 17.127 0.120166 167 168 169 170 171 172 173 174 175 1760.262 0.640 1.517 3.355 10.419 15.706 17.127 0.120 0.262 0.640 1.517177 178 179 180 181 182 183 184 185 186 1873.355 10.419 15.706 17.127 0.120 0.262 0.640 1.517 3.355 10.419 15.706188 189 190 191 192 193 194 195 196 197 19817.127 0.120 0.262 0.640 1.517 3.355 10.419 15.706 17.127 0.120 0.262199 200 201 202 203 204 205 206 207 208 2090.640 1.517 3.355 10.419 15.706 17.127 0.120 0.262 0.640 1.517 3.355210 211 212 213 214 215 216 217 218 219 22010.419 15.706 17.127 0.120 0.262 0.640 1.517 3.355 10.419 15.706 17.127221 222 223 224 225 226 227 228 229 230 2310.120 0.262 0.640 1.517 3.355 10.419 15.706 17.127 0.120 0.262 0.640232 233 234 235 236 237 238 239 240 241 2421.517 3.355 10.419 15.706 17.127 0.120 0.262 0.640 1.517 3.355 10.419243 244 245 246 247 248 249 250 251 252 25315.706 17.127 0.120 0.262 0.640 1.517 3.355 10.419 15.706 17.127 0.120254 255 256 257 258 259 260 261 262 263 2640.262 0.640 1.517 3.355 10.419 15.706 17.127 0.120 0.262 0.640 1.517265 266 267 268 269 270 271 272 273 274 2753.355 10.419 15.706 17.127 0.120 0.262 0.640 1.517 3.355 10.419 15.706276 277 278 279 280 281 282 283 284 285 28617.127 0.120 0.262 0.640 1.517 3.355 10.419 15.706 17.127 0.137 0.385287 288 289 290 291 292 293 294 295 296 2970.932 2.157 4.121 8.166 14.418 16.897 0.137 0.385 0.932 2.157 4.121298 299 300 301 302 303 304 305 306 307 3088.166 14.418 16.897 0.137 0.385 0.932 2.157 4.121 8.166 14.418 16.897309 310 311 312 313 314 315 316 317 318 3190.137 0.385 0.932 2.157 4.121 8.166 14.418 16.897 0.137 0.385 0.932320 321 322 323 324 325 326 327 328 329 3302.157 4.121 8.166 14.418 16.897 0.137 0.385 0.932 2.157 4.121 8.166331 332 333 334 335 336 337 338 339 340 34114.418 16.897 0.137 0.385 0.932 2.157 4.121 8.166 14.418 16.897 0.137342 343 344 345 346 347 348 349 350 351 3520.385 0.932 2.157 4.121 8.166 14.418 16.897 0.137 0.385 0.932 2.157353 354 355 356 357 358 359 360 361 362 3634.121 8.166 14.418 16.897 0.137 0.385 0.932 2.157 4.121 8.166 14.418364 365 366 367 368 369 370 371 372 373 37416.897 0.137 0.385 0.932 2.157 4.121 8.166 14.418 16.897 0.137 0.385375 376 377 378 379 380 381 382 383 384 3850.932 2.157 4.121 8.166 14.418 16.897 0.137 0.385 0.932 2.157 4.121386 387 388 389 390 391 392 393 394 395 3968.166 14.418 16.897 0.137 0.385 0.932 2.157 4.121 8.166 14.418 16.897397 398 399 400 401 402 403 404 405 406 4070.137 0.385 0.932 2.157 4.121 8.166 14.418 16.897 0.137 0.385 0.932408 409 410 411 4122.157 4.121 8.166 14.418 16.897attr(,"label")[1] "Fitted values (g)"> residuals(fm3)1 2 3 4 5 6 7 8NA NA NA NA NA -0.81724 -2.24772 -0.732039 10 11 12 13 14 15 160.44774 0.99485 -0.01627 -0.02870 0.05209 0.41153 -0.79366 -1.7572417 18 19 20 21 22 23 24-1.45772 1.07274 0.99072 -0.01227 -0.00670 -0.05891 0.34153 0.0863425 26 27 28 29 30 31 32-0.91724 -0.67772 3.99797 4.28854 5.05482 -0.01527 0.00130 0.1180933 34 35 36 37 38 39 40-0.38847 -1.48366 -2.36724 -2.13772 1.00797 -1.23396 -2.75138 -0.0192741 42 43 44 45 46 47 48-0.02470 0.12209 0.24153 1.04634 -1.03724 -1.04772 3.36834 -0.0142749 50 51 52 53 54 55 560.03930 -0.02691 -0.17847 0.14634 -1.44724 -1.52772 -0.35203 1.4868457 58 59 60 61 62 63 643.17632 -0.01827 -0.02270 0.04109 -0.25847 0.22634 -2.10724 -1.3177265 66 67 68 69 70 71 721.98604 0.96822 -0.01727 -0.02470 0.01609 -0.29847 -0.71366 -1.7872473 74 75 76 77 78 79 80-1.14772 -1.23203 2.32021 2.92402 0.01073 0.04030 -0.02491 -0.0484781 82 83 84 85 86 87 880.52634 2.19276 1.19228 2.69797 0.03104 0.51632 0.00773 0.1063089 90 91 92 93 94 95 960.17109 0.07153 0.18634 0.35276 -0.88772 4.77797 1.11774 10.6140297 98 99 100 101 102 103 1040.01073 0.08130 0.40009 0.73153 0.16634 -0.13724 1.53228 1.58797105 106 107 108 109 110 111 1127.86934 4.73482 0.03373 0.05930 0.45509 0.12153 0.98634 3.66276113 114 115 116 117 118 119 120-1.04772 1.42797 -0.93606 5.04402 0.01873 0.03030 0.20609 0.28153121 122 123 124 125 126 127 128-0.26366 -0.02724 0.83228 1.74797 0.02687 0.68572 0.01873 0.09130129 130 131 132 133 134 135 1360.36809 0.42153 0.31634 0.57276 1.52228 3.84797 -1.47226 13.51572137 138 139 140 141 142 143 1440.02473 0.06830 0.07309 -0.09847 -0.21366 -0.25724 -1.00772 0.45797145 146 147 148 149 150 151 1523.38604 5.81675 0.00973 0.05730 0.36409 0.57153 0.21634 -2.08724153 154 155 156 157 158 159 160-0.03772 -0.06203 2.10024 5.61482 -0.07327 -0.12571 -0.36726 -0.53373161 162 163 164 165 166 167 168-1.55813 -6.30167 -4.66844 -6.72407 -0.08527 -0.14971 -0.37209 -0.46373169 170 171 172 173 174 175 176-1.63980 -3.69048 -5.39225 -6.03907 -0.07627 -0.11571 -0.27959 -0.74206177 178 179 180 181 182 183 184-1.71313 -6.67048 -4.83058 -1.09990 -0.07127 -0.16471 -0.41259 -0.68373185 186 187 188 189 190 191 192-2.00080 -4.43048 -5.12058 -6.21597 -0.08127 -0.14071 -0.36842 -0.85873193 194 195 196 197 198 199 200-0.96480 -4.93548 -5.76891 -8.23907 -0.09127 -0.16971 -0.38909 -0.97539201 202 203 204 205 206 207 208-2.29313 -5.58881 -9.43391 -8.54407 -0.07927 -0.11671 -0.23476 -0.75706209 210 211 212 213 214 215 216-1.86147 -4.17048 -4.59388 -8.24740 -0.08227 -0.13471 -0.29992 -0.52306217 218 219 220 221 222 223 224-1.07313 -1.91281 -6.73225 -5.49540 -0.05027 -0.05371 -0.03926 0.38461225 226 227 228 229 230 231 232-0.38980 -2.27548 -0.00558 2.76090 -0.05227 -0.00971 -0.05959 0.49694233 234 235 236 237 238 239 240-0.68147 -1.61881 -1.22058 5.51590 -0.04327 -0.03771 -0.29876 0.22294241 242 243 244 245 246 247 2481.16920 1.23789 4.61112 4.27460 -0.02127 -0.06371 -0.14892 -0.31206249 250 251 252 253 254 255 256-0.55480 -3.05548 -0.56391 0.05927 -0.05227 -0.02971 -0.20409 -0.07373257 258 259 260 261 262 263 264-0.09480 -2.21048 3.70112 -1.46573 -0.05727 -0.05271 0.10074 -0.24873265 266 267 268 269 270 271 2720.53520 -1.32681 -1.21558 1.96760 0.01273 0.04129 0.47691 0.66294273 274 275 276 277 278 279 2800.18187 2.74119 0.08442 -2.35240 -0.03927 -0.00671 0.12474 -0.42373281 282 283 284 285 286 287 288-0.30313 -2.31381 8.71842 1.79090 -0.02776 -0.00104 0.23005 0.18344289 290 291 292 293 294 295 296-1.25117 1.37221 -1.73490 1.73667 -0.04196 -0.04654 -0.17329 0.36344297 298 299 300 301 302 303 304-1.60284 -3.04945 -5.84320 -2.72333 -0.04896 0.22830 0.38338 0.86511305 306 307 308 309 310 311 3121.72883 -0.74945 -3.08650 -0.01333 -0.04824 0.21180 0.14338 0.91844313 314 315 316 317 318 319 320-0.16284 -2.13279 -3.98153 0.90664 -0.03566 -0.00954 0.99005 0.05011321 322 323 324 325 326 327 3280.64383 0.97388 1.42180 1.21164 -0.02720 0.09846 0.37505 1.79844329 330 331 332 333 334 335 3360.18383 -0.13445 1.66513 2.67664 -0.03402 0.02963 0.73171 -0.76656337 338 339 340 341 342 343 344-1.11950 -1.32112 1.79180 2.17664 -0.06027 -0.01304 -0.18662 0.09011345 346 347 348 349 350 351 3520.37383 -2.49112 1.72680 2.03504 0.01178 0.30213 0.64005 1.65677353 354 355 356 357 358 359 3600.69050 3.48721 2.95850 1.00004 0.01680 0.20930 0.26838 0.98844361 362 363 364 365 366 367 368-0.31784 -0.74945 -0.83820 3.96334 -0.01280 0.36546 0.52671 3.60177369 370 371 372 373 374 375 3761.87550 0.80555 2.65350 0.92004 0.04150 0.49596 0.45005 1.47178377 378 379 380 381 382 383 3841.07217 -2.97612 1.36180 4.64501 0.00218 0.07096 0.65171 1.89844385 386 387 388 389 390 391 3920.38883 -0.00445 4.29680 1.05834 0.02574 0.38880 0.04338 1.35511393 394 395 396 397 398 399 4000.38883 -0.38279 3.70013 -0.94999 -0.02653 0.07113 0.43838 -0.01156401 402 403 404 405 406 407 4081.70883 0.63721 -2.18320 0.88834 0.00904 0.17880 0.54671 0.44511409 410 411 4122.22216 -2.03445 1.99350 0.05004attr(,"std")[1] NA NA NA NA NA 2.0514 3.0228 3.7679 4.1905 4.3895[11] 0.0575 0.1274 0.2786 0.5909 1.1714 2.0514 3.0228 4.1905 4.3895 0.0575[21] 0.1274 0.2786 0.5909 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575[31] 0.1274 0.2786 0.5909 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575[41] 0.1274 0.2786 0.5909 1.1714 2.0514 3.0228 4.1905 0.0575 0.1274 0.2786[51] 0.5909 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786[61] 0.5909 1.1714 2.0514 3.0228 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[71] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[81] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[91] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[101] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[111] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[121] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[131] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[141] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1274 0.2786 0.5909[151] 1.1714 2.0514 3.0228 3.7679 4.1905 4.3895 0.0575 0.1137 0.2495 0.5324[161] 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919[171] 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749[181] 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137[191] 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324[201] 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919[211] 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749[221] 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137[231] 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324[241] 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919[251] 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749[261] 0.0575 0.1137 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137[271] 0.2495 0.5324 1.0689 2.8919 4.1469 4.4749 0.0575 0.1137 0.2495 0.5324[281] 1.0689 2.8919 4.1469 4.4749 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348[291] 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219[301] 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596[311] 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251[321] 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348[331] 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219[341] 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596[351] 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251[361] 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348[371] 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219[381] 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596[391] 0.3469 0.7251 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251[401] 1.2806 2.3348 3.8468 4.4219 0.0644 0.1596 0.3469 0.7251 1.2806 2.3348[411] 3.8468 4.4219attr(,"label")[1] "Residuals (g)"> summary(fm3)Generalized nonlinear least squares fitModel: weight ~ SSlogis(Time, Asym, xmid, scal)Data: SoybeanAIC BIC logLik987 1007 -489Variance function:Structure: Power of variance covariateFormula: ~fitted(.)Parameter estimates:power0.878Coefficients:Value Std.Error t-value p-valueAsym 17.4 0.525 33.1 0xmid 51.9 0.598 86.8 0scal 7.6 0.142 54.0 0Correlation:Asym xmidxmid 0.788scal 0.488 0.842Standardized residuals:Min Q1 Med Q3 Max-2.3066 -0.6545 -0.0019 0.5012 4.9676Residual standard error: 0.369Degrees of freedom: 407 total; 404 residual>> options(op)# revert when this file is source()d>> proc.time()user system elapsed0.461 0.085 0.549