[R] help on lme extraction
Dear R list, I need some help in extracting comparisons in the result of lme. I have a data set similar to the example data, Orthodont, using patient subject as a random effect and did something below: library(nlme) library(gregmisc) data(Orthodont) Orthodont$AgeGroup - gtools::quantcut(Orthodont$age) fm2 - lme(distance ~ AgeGroup + Sex + AgeGroup*Sex, data = Orthodont, random = ~1|Subject) fit.contrast(fm2, Sex, c(-1,1), conf=0.95) fit.contrast(fm2, AgeGroup, rbind(1 vs 2=c(-1,1,0,0), 2 vs 3=c(0,-1,1,0)), conf=0.95) But how can I compare different age groups among Male, Female or between Male and Female as illustrated below: ## among Male Male Female [1,] -1 0 [2,]1 0 [3,]0 0 [4,]0 0 ## among Female Male Female [1,]0 0 [2,]0 -1 [3,]0 0 [4,]0 1 ## between Male and Female Male Female [1,] -1 0 [2,]0 0 [3,]0 0 [4,]0 1 I'll greatly appreciate it if you may help! JP Jin Ph.D. Bioinformatics scientist Center for Bioinformatics UNC at Chapel Hill Chapel Hill, NC US [[alternative HTML version deleted]] __ R-help@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.
[R] how to use glm for a time course data set
Dear list, I used glm to analyze the effect of treatment, measurement-methods etc. on lesion size in a time course experiments. Could anyone points me out how to extract detailed comparisons of interest? For example: Measurement.T2.M6 vs. Measurement.T2.Baseline, Or even Measurement.T2.M6.Treatment vs. Measurement.T2.M6.placebo (I did not include Treatment as a factor in the query below yet). Thanks for your help (data was attached)! Jp Jin summary(glm(data$Lesion.Size~Time+Measurement+Time*Measurement, data=data)) Call: glm(formula = data$Lesion.Size ~ Time + Measurement + Time * Measurement, data = data) Deviance Residuals: Min 1Q Median 3Q Max -5344.9 -2494.8 -1289.5981.7 29248.7 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 1352.7 1180.6 1.146 0.2546 Timem12 708.4 1669.7 0.424 0.6723 Timem6 630.6 1669.7 0.378 0.7064 MeasurementT2 4079.8 1669.7 2.443 0.0163 * Timem12:MeasurementT2 -2400.5 2361.3 -1.017 0.3117 Timem6:MeasurementT2 -1763.5 2361.3 -0.747 0.4569 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 25090570) Null deviance: 2787055253 on 107 degrees of freedom Residual deviance: 2559238182 on 102 degrees of freedom AIC: 2154.4 Number of Fisher Scoring iterations: 2 ID Treatment TimeMeasurement Relapse Lesion.Size N01 placebo baselineT1 yes 3214 N01 placebo baselineT2 yes 6695 N01 placebo m6 T1 yes 2682 N01 placebo m6 T2 yes 6784 N01 placebo m12 T1 yes 2666 N01 placebo m12 T2 yes 8433.5 N05 placebo baselineT1 yes 1232 N05 placebo baselineT2 yes 1913.25 N05 placebo m6 T1 yes 652 N05 placebo m6 T2 yes 1909 N05 placebo m12 T1 yes 995 N05 placebo m12 T2 yes 1294.5 N07 statin baselineT1 no 1378 N07 statin baselineT2 no 3786.75 N07 statin m6 T1 no 701 N07 statin m6 T2 no 1382.25 N07 statin m12 T1 no 818 N07 statin m12 T2 no 1098.5 N08 placebo baselineT1 no 3522 N08 placebo baselineT2 no 8714.25 N08 placebo m6 T1 no 4115 N08 placebo m6 T2 no 8944.75 N08 placebo m12 T1 no 3456 N08 placebo m12 T2 no 9093.25 N10 placebo baselineT1 no 87 N10 placebo baselineT2 no 302.25 N10 placebo m6 T1 no 101 N10 placebo m6 T2 no 228.25 N10 placebo m12 T1 no 64 N10 placebo m12 T2 no 221.25 N11 statin baselineT1 no 406.8 N11 statin baselineT2 no 6456.6 N11 statin m6 T1 no 1528 N11 statin m6 T2 no 7726 N11 statin m12 T1 no 2898 N11 statin m12 T2 no 6880.75 N12 statin baselineT1 no 721.6 N12 statin baselineT2 no 21421.8 N12 statin m6 T1 no 11464 N12 statin m6 T2 no 20275.3 N12 statin m12 T1 no 8 N12 statin m12 T2 no 10187.3 N14 statin baselineT1 no 418 N14 statin baselineT2 no 1331.75 N14 statin m6 T1 no 476 N14 statin m6 T2 no 581.25 N14 statin m12 T1 no 536 N14 statin m12 T2 no 372.2 N15 placebo baselineT1 no 8103.5 N15 placebo baselineT2 no 34681.1 N15 placebo m6 T1 no 8710 N15 placebo m6 T2 no 14595.5 N15 placebo m12 T1 no 7215 N15 placebo m12 T2 no 12651.3 N16 placebo baselineT1 yes 644 N16 placebo baselineT2 yes 1253.25 N16 placebo m6 T1 yes 767 N16 placebo m6 T2 yes 1366.25 N16 placebo m12 T1 yes 1961 N16 placebo m12 T2 yes 1433 N17 statin baselineT1 no 56 N17 statin baselineT2 no 87.5 N17 statin m6 T1 no 0 N17 statin m6 T2 no 64.5 N17 statin m12 T1 no 0 N17 statin m12 T2 no 84.5 N19 statin baselineT1 no 0 N19 statin baselineT2 no 856.1 N19 statin m6 T1 no 183 N19 statin m6 T2 no 4065 N19 statin m12 T1 no 1092 N19 statin m12 T2
