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How to plot survival data from multiple trials (simulations)?
6 messages · Zheng Lu, Lancaster, Robert (Orbitz), Weidong Gu
I'm assuming you want to plot the Kaplan-Meier curves. First, load your data into a data.frame, e.g. surv_data It looks like ST is your survival time and ind is your event indicator. The following code should get you started: # create your survival object: mySurv = Surv(surv_data$ST,surv_data$ind) # use survfit, which will generate KM curves: survFit = survfit(mySurv~surv_data$GROUP) # plot your curves. plot(survFit,conf.int=TRUE,xlab="time",ylab="survival pct") -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Zheng Lu Sent: Friday, October 28, 2011 10:30 PM To: r-help at r-project.org Subject: [R] How to plot survival data from multiple trials (simulations)? Dear all: Could anyone please provide some R codes to plot the below survival data to compare two groups (0 vs 1) after 2 simulations (TRL)? need 95% prediction interval on the plot from these 2 trials. I would like to simulate 1000 trials later. Thanks a lot for your great help and consideration! yan TRL ID ECOG BASE PTR8 GROUP POP ST ind 1 1 1 1 2.2636717 0.255634126 1 1 99.4 F 3 1 2 1 24.7719223 0.756458142 0 1 8.1 T 5 1 3 0 4.7685832 0.908777937 1 0 2.6 T 7 1 4 0 2.5934492 -0.231564522 1 1 7.4 T 9 1 5 0 4.7309141 -2.455991696 0 1 0.4 T 11 1 6 1 3.5904766 -0.459694803 1 1 13.1 T 13 1 7 1 4.8592495 0.983131140 1 1 17.8 T 15 1 8 1 3.1308760 -1.136462783 0 0 10.6 T 17 1 9 1 5.8127637 -0.131647588 0 1 1.2 T 19 1 10 0 4.0875668 -3.567509428 0 1 0.4 T 21 1 11 1 14.7112528 0.900416367 1 1 15.2 T 23 1 12 0 6.7290298 -0.140283251 0 0 8.5 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 25 1 13 0 6.6118789 -0.095603854 0 1 13.8 T 27 1 14 1 1.1191479 0.735691765 1 1 60.5 F 29 1 15 0 11.9169275 0.796172293 0 0 40.1 F 31 1 16 1 6.7940011 0.845746271 1 1 68.1 F 33 1 17 0 4.7380330 0.582527179 1 1 11.7 T 35 1 18 0 12.0571049 0.165637187 0 0 25.0 T 37 1 19 1 3.1922217 0.891862148 1 1 34.0 T 39 1 20 0 10.6253830 -0.747701704 0 1 7.8 T 41 1 21 0 2.0178336 -2.732716143 0 1 0.8 T 43 1 22 1 13.8066137 0.706372607 0 1 58.2 F 45 1 23 1 11.8844261 0.842735359 1 1 13.9 T 47 1 24 1 3.9546421 0.193353044 0 1 2.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 49 1 25 0 27.0913396 0.970400135 1 1 19.1 T 51 1 26 1 12.0249672 0.886403017 1 1 27.1 T 53 1 27 1 5.9453281 0.964694968 1 1 21.2 T 55 1 28 0 6.8084911 -1.333850454 1 0 4.1 T 57 1 29 1 8.3642227 -0.024960757 0 1 4.4 T 59 1 30 0 26.6382483 0.714020234 0 0 3.9 T 61 1 31 1 13.1107410 0.372041597 0 1 26.2 T 63 1 32 0 4.2271255 0.056569282 1 1 14.3 T 65 1 33 0 17.7269456 0.252550311 0 0 11.2 T 67 1 34 1 3.6215522 -0.282323084 0 0 0.3 T 69 1 35 1 19.3787770 0.349288143 0 1 5.2 T 71 1 36 0 8.9546567 0.945492048 1 1 15.2 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 73 1 37 0 2.7796959 -3.119155682 0 0 12.3 T 75 1 38 0 9.4029912 -0.793046460 0 1 1.2 T 77 1 39 1 7.8146429 0.888593758 1 1 8.0 T 79 1 40 0 9.6419102 0.525301532 1 1 22.4 T 81 1 41 1 3.3174969 0.915870306 1 1 24.7 T 83 1 42 1 12.4030358 0.661856980 1 1 16.4 T 85 1 43 1 24.2982862 0.710967270 0 1 5.5 T 87 1 44 0 10.4332028 0.940833126 1 0 2.9 T 89 1 45 0 4.7520799 0.897518558 1 1 32.6 T 91 1 46 0 2.7028663 -3.484128492 0 1 0.2 T 93 1 47 1 2.7572158 0.890976979 1 0 30.9 T 95 1 48 0 7.2240161 -0.377073350 0 0 3.7 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 97 1 49 0 20.6156368 0.500864314 0 1 12.2 T 99 1 50 1 12.8547093 0.982784519 1 1 54.4 F 2 2 1 1 3.0862631 0.931988949 1 1 199.2 F 4 2 2 1 18.6633707 0.540651036 0 1 8.1 T 6 2 3 0 5.5728260 -1.851336117 1 0 3.0 T 8 2 4 0 4.0740408 0.021119280 1 1 10.1 T 10 2 5 0 14.2396242 0.465013972 0 1 6.6 T 12 2 6 1 37.5234448 0.986992132 1 1 30.5 T 14 2 7 1 11.2925748 0.922905093 1 1 14.0 T 16 2 8 1 15.2298842 0.459418082 0 0 12.6 T 18 2 9 1 5.3266590 -1.487487920 0 1 0.3 T 20 2 10 0 11.7956270 0.606294774 0 1 26.9 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 22 2 11 1 26.0051377 0.823996317 1 1 8.6 T 24 2 12 0 4.7851855 -1.635216564 0 0 10.7 T 26 2 13 0 5.4896572 -1.085740446 0 1 3.8 T 28 2 14 1 15.0284557 0.981428564 1 1 56.1 F 30 2 15 0 15.3001584 -0.101949376 0 0 36.7 T 32 2 16 1 4.1838899 -0.002416447 1 1 26.0 T 34 2 17 0 1.9213881 0.678721863 1 1 15.5 T 36 2 18 0 22.0870166 0.682030393 0 0 18.8 T 38 2 19 1 7.8815644 0.938210236 1 1 25.9 T 40 2 20 0 6.8308086 -0.774314088 0 1 8.5 T 42 2 21 0 6.0056206 -0.656448295 0 1 5.4 T 44 2 22 1 11.9301049 0.137476151 0 1 32.2 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 46 2 23 1 4.4453597 0.932378925 1 1 18.3 T 48 2 24 1 7.0352655 0.142463064 0 1 2.4 T 50 2 25 0 22.1603315 0.990013687 1 1 23.5 T 52 2 26 1 1.7582992 0.041687569 1 1 13.6 T 54 2 27 1 4.0864310 0.893550143 1 1 18.7 T 56 2 28 0 3.7564158 0.149721394 1 0 3.1 T 58 2 29 1 23.7880592 0.312680371 0 1 4.0 T 60 2 30 0 7.3082204 0.084729300 0 0 3.4 T 62 2 31 1 29.8669157 0.779756301 0 1 24.3 T 64 2 32 0 6.7967624 0.228897567 1 1 15.8 T 66 2 33 0 9.0048160 -1.073334969 0 0 9.5 T 68 2 34 1 9.3920052 0.183028557 0 0 0.3 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 70 2 35 1 17.0794700 0.575865059 0 1 6.7 T 72 2 36 0 5.8638675 0.986021171 1 1 18.2 T 74 2 37 0 12.7073727 0.808851125 0 0 11.6 T 76 2 38 0 6.6391834 -0.515246589 0 1 1.5 T 78 2 39 1 4.0731162 0.640324530 1 1 6.9 T 80 2 40 0 8.1501724 0.963706289 1 1 37.9 T 82 2 41 1 7.1095450 0.852592536 1 1 19.9 T 84 2 42 1 6.3169479 0.686874101 1 1 23.2 T 86 2 43 1 12.8719503 -0.442671821 0 1 2.5 T 88 2 44 0 19.2469239 0.982064666 1 0 3.3 T 90 2 45 0 6.7743672 0.724107074 1 1 24.1 T 92 2 46 0 7.9332652 0.050580084 0 1 5.9 T TRL ID ECOG BASE PTR8 GROUP POP ST ind 94 2 47 1 0.6997334 -0.146007844 1 0 23.7 T 96 2 48 0 14.6486847 0.723251604 0 0 4.5 T 98 2 49 0 4.1576131 0.232732832 0 1 15.6 T 100 2 50 1 7.2583626 0.811803286 1 1 49.0 F ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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1 day later
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One option is to use table to get the number of repeats tab<-table(tr1$time)==3 time3<-names(tab)[tab] tr1[tr1$time%in%time3,] Weidong Gu
On Sun, Oct 30, 2011 at 5:10 PM, Zheng Lu <luyan6 at hotmail.com> wrote:
With the following dataset, trl =1, 2,3, how to extract data with the time repeated 3 times. For example, I am only interested in the data records with time repeated 3 times. time=0.1 only has 1 time, we don't want it, ?time=0.3 only has two times, we don't want it, and so on. Thanks a lot. time surv trl 1 0.0 0.990 1 124 0.0 0.995 2 250 0.0 0.980 3 125 0.1 0.990 2 2 0.2 0.985 1 126 0.2 0.985 2 251 0.2 0.975 3 3 0.3 0.980 1 127 0.3 0.980 2 4 0.4 0.975 1 128 0.4 0.975 2 252 0.4 0.965 3 5 0.5 0.970 1 6 0.6 0.965 1 129 0.6 0.970 2 253 0.6 0.955 3 7 0.8 0.960 1 130 0.8 0.960 2 254 0.8 0.950 3 131 0.9 0.955 2 255 0.9 0.945 3 8 1.0 0.955 1 256 1.0 0.940 3 time surv trl 257 1.3 0.935 3 9 1.7 0.950 1 132 1.8 0.950 2 258 1.8 0.930 3 133 1.9 0.945 2 259 1.9 0.925 3 10 2.0 0.945 1 134 2.0 0.935 2 260 2.1 0.915 3 11 2.2 0.935 1 135 2.2 0.930 2 261 2.2 0.905 3 12 2.4 0.930 1 262 2.4 0.900 3 13 2.5 0.925 1 136 2.5 0.925 2 263 2.5 0.895 3 137 2.6 0.915 2 264 2.6 0.880 3 14 2.7 0.915 1 138 2.7 0.895 2 265 2.7 0.870 3 15 2.8 0.910 1 time surv trl 266 2.8 0.860 3 16 2.9 0.895 1 267 2.9 0.855 3 17 3.0 0.890 1 139 3.0 0.885 2 268 3.0 0.840 3 18 3.1 0.885 1 269 3.1 0.835 3 19 3.2 0.880 1 270 3.2 0.830 3 20 3.3 0.875 1 140 3.3 0.880 2 141 3.4 0.870 2 21 3.5 0.870 1 142 3.8 0.855 2 271 3.8 0.825 3 22 3.9 0.860 1 143 3.9 0.845 2 272 3.9 0.820 3 273 4.0 0.805 3 144 4.1 0.840 2 274 4.1 0.800 3 145 4.2 0.835 2 time surv trl 275 4.2 0.795 3 23 4.3 0.855 1 24 4.4 0.850 1 146 4.4 0.830 2 276 4.4 0.790 3 25 4.5 0.835 1 147 4.5 0.825 2 277 4.5 0.785 3 26 4.6 0.820 1 278 4.6 0.780 3 27 4.7 0.810 1 148 4.7 0.820 2 28 4.8 0.805 1 29 4.9 0.800 1 149 4.9 0.815 2 279 5.0 0.770 3 30 5.1 0.790 1 150 5.1 0.805 2 31 5.2 0.785 1 151 5.2 0.800 2 32 5.3 0.780 1 152 5.3 0.795 2 33 5.4 0.775 1 time surv trl 280 5.4 0.750 3 153 5.5 0.790 2 34 5.6 0.765 1 281 5.7 0.745 3 154 5.8 0.775 2 155 5.9 0.770 2 35 6.0 0.760 1 282 6.0 0.740 3 283 6.1 0.735 3 36 6.2 0.750 1 284 6.2 0.725 3 285 6.3 0.720 3 37 6.4 0.745 1 156 6.4 0.765 2 157 6.5 0.760 2 286 6.5 0.710 3 38 6.6 0.735 1 158 6.6 0.755 2 159 6.7 0.745 2 287 6.7 0.700 3 288 6.8 0.690 3 39 6.9 0.725 1 160 6.9 0.735 2 time surv trl 289 6.9 0.685 3 40 7.0 0.715 1 161 7.0 0.720 2 41 7.1 0.710 1 162 7.1 0.710 2 42 7.2 0.705 1 290 7.2 0.670 3 43 7.3 0.700 1 163 7.3 0.705 2 44 7.4 0.690 1 164 7.4 0.700 2 291 7.4 0.660 3 165 7.5 0.690 2 292 7.6 0.650 3 45 7.7 0.685 1 166 7.8 0.685 2 46 7.9 0.680 1 167 7.9 0.680 2 293 7.9 0.645 3 47 8.0 0.675 1 168 8.0 0.675 2 294 8.0 0.640 3 48 8.1 0.665 1 time surv trl 295 8.1 0.635 3 49 8.4 0.655 1 296 8.4 0.625 3 169 8.5 0.670 2 297 8.5 0.620 3 170 8.6 0.665 2 50 8.7 0.645 1 171 8.7 0.660 2 298 8.7 0.615 3 172 8.8 0.655 2 51 8.9 0.635 1 52 9.0 0.630 1 53 9.1 0.620 1 173 9.1 0.650 2 54 9.2 0.610 1 174 9.2 0.640 2 55 9.3 0.600 1 175 9.4 0.635 2 299 9.4 0.605 3 176 9.5 0.620 2 177 9.6 0.610 2 300 9.6 0.595 3 178 9.7 0.605 2 time surv trl 179 9.8 0.600 2 301 9.8 0.590 3 56 9.9 0.595 1 180 9.9 0.595 2 302 9.9 0.585 3 303 10.0 0.580 3 181 10.1 0.590 2 57 10.2 0.590 1 304 10.2 0.575 3 182 10.4 0.585 2 183 10.5 0.570 2 184 10.6 0.565 2 305 10.6 0.570 3 58 10.7 0.580 1 185 10.7 0.560 2 186 10.8 0.555 2 187 11.0 0.545 2 188 11.1 0.540 2 306 11.1 0.565 3 59 11.2 0.575 1 189 11.3 0.535 2 307 11.3 0.555 3 60 11.4 0.560 1 time surv trl 190 11.4 0.530 2 308 11.6 0.550 3 61 11.7 0.555 1 309 11.8 0.545 3 62 11.9 0.550 1 191 11.9 0.525 2 310 11.9 0.540 3 63 12.0 0.545 1 192 12.0 0.520 2 311 12.0 0.535 3 193 12.1 0.505 2 312 12.2 0.525 3 64 12.3 0.540 1 194 12.6 0.500 2 313 12.6 0.520 3 314 12.9 0.515 3 195 13.0 0.495 2 315 13.2 0.505 3 316 13.4 0.500 3 65 13.5 0.535 1 196 13.5 0.490 2 317 13.5 0.495 3 66 13.6 0.530 1 time surv trl 197 13.6 0.485 2 318 13.6 0.480 3 67 13.7 0.525 1 198 13.7 0.480 2 199 13.8 0.475 2 319 13.9 0.475 3 68 14.1 0.520 1 200 14.1 0.470 2 69 14.2 0.515 1 201 14.2 0.465 2 70 14.5 0.510 1 320 14.5 0.470 3 321 14.6 0.460 3 202 14.8 0.460 2 71 15.0 0.505 1 72 15.2 0.495 1 322 15.4 0.450 3 73 15.5 0.490 1 203 15.5 0.455 2 323 15.5 0.445 3 74 15.6 0.485 1 204 15.7 0.450 2 324 15.7 0.440 3 time surv trl 205 15.8 0.445 2 325 15.8 0.435 3 75 16.0 0.480 1 76 16.1 0.475 1 206 16.1 0.440 2 77 16.2 0.470 1 326 16.2 0.430 3 207 16.3 0.435 2 327 16.5 0.425 3 78 16.6 0.465 1 208 16.7 0.430 2 328 16.7 0.420 3 209 16.8 0.420 2 329 16.8 0.415 3 330 16.9 0.410 3 79 17.0 0.460 1 80 17.1 0.455 1 210 17.1 0.415 2 81 17.2 0.450 1 331 17.2 0.405 3 82 17.3 0.435 1 332 17.3 0.400 3 83 17.4 0.430 1 time surv trl 333 17.5 0.390 3 334 17.6 0.385 3 84 17.7 0.425 1 335 17.7 0.380 3 211 18.1 0.410 2 212 18.2 0.405 2 85 18.3 0.420 1 213 18.4 0.400 2 336 18.4 0.370 3 214 18.5 0.395 2 86 18.6 0.415 1 87 18.9 0.410 1 337 18.9 0.365 3 338 19.2 0.355 3 339 19.3 0.350 3 88 19.4 0.405 1 340 19.4 0.345 3 89 19.5 0.400 1 215 19.5 0.390 2 216 19.6 0.385 2 217 19.7 0.380 2 341 19.7 0.340 3 90 19.8 0.395 1 time surv trl 91 19.9 0.390 1 92 20.0 0.385 1 93 20.1 0.380 1 218 20.4 0.370 2 219 20.5 0.365 2 342 20.5 0.330 3 220 20.8 0.360 2 343 20.9 0.325 3 221 21.0 0.355 2 344 21.0 0.320 3 94 21.1 0.375 1 345 21.1 0.315 3 222 21.2 0.350 2 95 21.5 0.370 1 96 21.7 0.365 1 97 22.0 0.360 1 223 22.0 0.345 2 346 22.3 0.310 3 224 22.4 0.335 2 98 23.0 0.355 1 347 23.0 0.305 3 348 23.2 0.300 3 349 23.4 0.295 3 time surv trl 99 23.5 0.350 1 225 23.5 0.330 2 226 23.8 0.325 2 227 24.0 0.320 2 228 24.4 0.315 2 100 24.5 0.345 1 101 24.7 0.340 1 229 24.7 0.310 2 230 24.8 0.305 2 102 25.1 0.335 1 350 25.3 0.290 3 231 25.6 0.295 2 103 25.7 0.330 1 232 25.7 0.290 2 351 25.8 0.285 3 352 25.9 0.280 3 104 26.0 0.325 1 233 26.0 0.285 2 234 26.2 0.280 2 105 26.4 0.320 1 106 26.5 0.310 1 235 26.6 0.275 2 107 26.9 0.305 1 time surv trl 236 27.2 0.270 2 353 27.2 0.275 3 354 27.3 0.270 3 237 27.5 0.265 2 355 27.6 0.265 3 108 28.0 0.300 1 109 28.1 0.295 1 110 28.4 0.290 1 111 28.6 0.285 1 238 28.6 0.260 2 112 28.7 0.275 1 113 28.9 0.270 1 356 29.0 0.260 3 239 29.1 0.255 2 357 29.5 0.255 3 240 29.7 0.245 2 114 29.9 0.265 1 115 30.2 0.260 1 241 30.3 0.240 2 242 30.9 0.235 2 116 31.4 0.255 1 243 31.5 0.230 2 117 31.8 0.250 1 time surv trl 118 31.9 0.245 1 119 32.5 0.240 1 244 32.5 0.225 2 358 32.7 0.250 3 245 32.8 0.220 2 246 33.2 0.215 2 359 33.9 0.245 3 360 34.3 0.240 3 361 34.5 0.235 3 247 34.6 0.210 2 362 34.8 0.230 3 120 35.1 0.235 1 248 35.6 0.200 2 363 36.0 0.215 3 121 36.6 0.230 1 122 37.1 0.225 1 364 37.2 0.210 3 365 37.3 0.205 3 249 37.6 0.195 2 366 37.8 0.200 3 367 38.3 0.195 3 368 38.6 0.190 3 369 39.5 0.185 3 time surv trl 123 39.7 0.220 1 ? ? ? ?[[alternative HTML version deleted]]
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