plotGAMM function

GAMM plotting using ggplot2

plotGAMM(gammFit, smooth.cov, groupCovs = NULL, orderedAsFactor = F,
  rawOrFitted = F, plotCI = T, grouping = NULL)

Arguments

• gammFit: fitted gam model as produced by gamm4::gamm()
• smooth.cov: (character) name of smooth term to be plotted
• groupCovs: (character) name of group variable to plot by, if NULL (default) then there are no groups in plot
• orderedAsFactor: Disabled
• rawOrFitted: If FALSE (default) then only smooth terms are plotted; if rawOrFitted = "raw" then raw values are plotted against smooth; if rawOrFitted = "fitted" then fitted values are plotted against smooth
• plotCI: if TRUE (default) upper and lower confidence intervals are added at 2 standard errors above and below the mean
• grouping: (character) Name of variable that you want to use as the group argument in ggplot2::aes(), useful for better visualization of longitudinal data, (default is NULL)

Returns

Returns a ggplot object that can be visualized using the print() function

Examples

set.seed(1)
data <- data.frame(x = (seq(.25,25, .25) +rnorm(100)), group = rep(1:2, 5), z=rnorm(100),
              index.rnorm = rep(rnorm(50, sd = 50), 2), index.var = rep(1:50, 2))
data$y <- (data$x)*data$group*10 + rnorm(100, sd = 700) + data$index.rnorm + data$z
data$group <- ordered(data$group)

gamm <- gamm4::gamm4(y ~ + s(x) + s(x, by=group) + z + group, data=data, random = ~ (1|index.var))

plot <- plotGAMM(gammFit <- gamm, smooth.cov <- "x", groupCovs = "group",
                    plotCI <- T, rawOrFitted = "raw", grouping = "index.var")

plot2 <- plotGAMM(gammFit <- gamm, smooth.cov <- "x", groupCovs = "group",
                  plotCI <- T, rawOrFitted = "fitted", grouping = "index.var")

See Also

Other Plotting: plotGAM