Thierry, Thank you so much for the help! That method worked perfectly!
Cheers, Alyse ________________________________________ From: ONKELINX, Thierry [[email protected]] Sent: Tuesday, April 08, 2014 3:38 AM To: Yeager, Alyse D; [email protected] Subject: RE: [R-sig-eco] Mixed Effects Model with Post-hoc interaction contrasts (lme + glht) Dear Alyse, The easiest way it to create a new variable that has the interaction. E.g. apa3$TimeReach <- interaction(apa3$Time, apa3$Reach). Then refit your model with this variable instead of Time and Reach. lme(APA~ TimeReach, random=~1|Station, method="REML", data=apa3) The coefficient can be different due to the change in parameterization, but the model fit will be identical. Now you can use glht with user defined contracts to make the required comparisons. See the examples in ?glht on how to do that. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium + 32 2 525 02 51 + 32 54 43 61 85 [email protected] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -----Oorspronkelijk bericht----- Van: [email protected] [mailto:[email protected]] Namens Yeager, Alyse D Verzonden: maandag 7 april 2014 20:11 Aan: [email protected] Onderwerp: [R-sig-eco] Mixed Effects Model with Post-hoc interaction contrasts (lme + glht) Hello all, I am a Master's student seeking help to run a mixed effects model with a post-hoc (Tukey) analysis on my thesis data. I am having difficulty setting contrasts for the post-hoc analysis so that it only compares 3 specific interactions (REF vs TRT @PRE), (REF vs TRT @WK4), and (REF vs TRT @WK8). I need to compare enzyme activity (APA) from periphyton on rocks in a reference (REF) and treatment (TRT) "reach" of a stream. I have 3 "stations" within each reach (UP, MID, DWN) where 4 replicate rocks were collected, and I have 3 "time" points to observe differences due to the treatment (PRE, WK4, WK8). Thus, 48 samples total. I have set up a mixed effects model using "reach" and "time" as the fixed effects and "station" as the random effect. My mixed effects model was run as follows using the "nlme" package: lme(APA~1+Time+Reach+Time*Reach, random=~1|Station, method="REML", data=apa3) Here is the output: Linear mixed-effects model fit by REML Data: apa3 AIC BIC logLik -302.3262 -284.809 159.1631 Random effects: Formula: ~1 | Station (Intercept) Residual StdDev: 3.833552e-07 0.01938121 Fixed effects: APA ~ 1 + Time + Reach + Time * Reach Value Std.Error DF t-value p-value (Intercept) 0.028333333 0.005594873 64 5.064160 0.0000 TimeWK4 -0.003333333 0.007912346 64 -0.421283 0.6750 TimeWK8 -0.003333333 0.007912346 64 -0.421283 0.6750 ReachTRT 0.003333333 0.007912346 64 0.421283 0.6750 TimeWK4:ReachTRT 0.023333333 0.011189747 64 2.085242 0.0410 TimeWK8:ReachTRT 0.025833333 0.011189747 64 2.308661 0.0242 Correlation: (Intr) TimWK4 TimWK8 RchTRT TWK4:R TimeWK4 -0.707 TimeWK8 -0.707 0.500 ReachTRT -0.707 0.500 0.500 TimeWK4:ReachTRT 0.500 -0.707 -0.354 -0.707 TimeWK8:ReachTRT 0.500 -0.354 -0.707 -0.707 0.500 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -2.14984854 -0.73094850 -0.08599394 0.42996971 2.36483339 Number of Observations: 72 Number of Groups: 3 >From this output, I gathered that there was a significant interaction between >Reach and Time. The issue I am attempting to address is the manner in which I setup a post-hoc test comparing only the two reaches on one specific time point. We are not interested in comparing, for instance, REF@WK4 to TRT@WK8, but only (REF & TRT @PRE), (REF & TRT @WK4), and (REF & TRT @WK8). I have been attempting to set up this comparison using glht in the "multcomp" package, but cannot figure out how to prepare a contrast statement with these interactions only. Anyone who can set up an interaction contrast statement, please help. Thank you, Alyse [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. 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