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2.8 - 2.8 Summary of Important R code

by Mark Greenwood and Katharine Banner

The main components of R code used in this chapter follow with components to modify in red, remembering that any R packages mentioned need to be installed and loaded for this code to have a chance of working:

  • • MODELNAME=lm(Y~X,data=DATASETNAME)
    • ◦ Provides numerical summaries of all variables in the data set.
    • ◦ Here it is used to fit the reference-coded One-Way ANOVA model with Y as the response variable and X as the grouping variable, storing the estimated model object in MODELNAME.
  • • MODELNAME=lm(Y~X-1,data=DATASETNAME)
    • ◦ Fits the cell means version of the One-Way ANOVA model.
  • • summary(MODELNAME))
    • ◦ Generates model summary information including the estimated model coefficients, SEs, t-tests, and p-values.
  • • anova(MODELNAME)
    • ◦ Generates the ANOVA table but must only be run on the reference-coded version of the model.
    • ◦ Results are incorrect if run on the cell-means model since the reduced model under the null is that the mean of all the observations is 0!
  • • pf(FSTATISTIC,df1=NUMDF,df2=DENDF,lower.tail=F)
    • ◦ Finds the p-value for an observed F-statistic with NUMDF and DENDF degrees of freedom.
  • • par(mfrow=c(2,2)); plot(MODELNAME)
    • ◦ Generates four diagnostic plots including the Residuals vs Fitted and Normal Q-Q plot.
  • • plot(allEffects(MODELNAME))
    • ◦ Plots the estimated model.
    • ◦ Requires the effects package be loaded.
  • • Tm2=glht(MODELNAME,linfct=mcp(X="Tukey"); confint(Tm2); plot(Tm2); cld(Tm2)
    • ◦ Requires the multcomp package to be installed and loaded.
    • ◦ Can only be run on the reference-coded version of the model.
    • ◦ Generates the text output and plot for Tukey's HSD as well as the compact letter display.

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