mgcViz (version 0.2.1)

qq.gamViz: QQ plots for gam model residuals

Description

Takes a fitted gam object, converted using getViz, and produces QQ plots of its residuals (conditional on the fitted model coefficients and scale parameter). If the model distributional assumptions are met then usually these plots should be close to a straight line (although discrete data can yield marked random departures from this line).

Usage

# S3 method for gamViz
qq(
  o,
  rep = 10,
  level = 0.8,
  method = "auto",
  type = "auto",
  CI = "none",
  worm = FALSE,
  showReps = FALSE,
  sortFun = NULL,
  discrete = NULL,
  ngr = 1000,
  xlim = NULL,
  ylim = NULL,
  a.qqpoi = list(),
  a.ablin = list(),
  a.cipoly = list(),
  a.replin = list(),
  ...
)

Value

An object of class c("qqGam", "plotSmooth", "gg").

Arguments

o

an object of class gamViz, the output of a getViz() call.

rep

how many replicate datasets to generate to simulate quantiles of the residual distribution. Relevant only if method is set to "simul1" or "simul2".

level

the level of the confidence intervals (e.g. 0.9 means 90% intervals).

method

the method used to calculate the QQ-plot and, possibly, the confidence intervals. If set to ("tunif") "tnormal" the residuals are transformed to (uniform) normal, for which analytic expression for the confidence intervals are available. If set to "simul1" or "simul2" the theoretical QQ-line is constructed by simulating residuals from the model. Method "simul2" does not produce confidence intervals. If set to "normal" no simulation or transformation is performed, and a simple normal QQ-plot is produced. If set to "auto" the method used to produce the QQ-plot is determined automatically.

type

the type of residuals to be used. See residuals.gamViz.

CI

the type of confidence intervals to be plotted. If set to "none" they are not added, if set to "normal" they will be based on the assumption that the theoretical quantile distribution is Gaussian and if set to "quantile" they will be sample quantiles of simulated responses from the model.

worm

if TRUE a worm-plot (a de-trended QQ-plot) is plotted.

showReps

if TRUE all the QQ-lines corresponding to the simulated (model-based) QQ-plots.

sortFun

the function to be used for sorting the residuals. If left to NULL it will be set to function(.x) sort(.x, method = "quick") internally.

discrete

if TRUE the QQ-plot is discretized into ngr bins before plotting, in order to save plotting time (when the number of observations is large). If left to NULL, the discretization is used if there are more than 10^4 observations.

ngr

number of bins to be used in the discretization.

xlim

if supplied then this pair of numbers are used as the x limits for the plot.

ylim

if supplied then this pair of numbers are used as the y limits for the plot.

a.qqpoi

list of arguments to be passed to ggplot2::geom_point, which plots the main QQ-plot.

a.ablin

list of arguments to be passed to ggplot2::geom_abline, which adds the reference line.

a.cipoly

list of arguments to be passed to ggplot2::geom_polygon, which add the confidence intervals.

a.replin

list of arguments to be passed to ggplot2::geom_line, which adds a line for each simulated QQ-plot.

...

currently unused.

Details

Here method = "simul1" corresponds to the algorithm described in section 2.1 of Augustin et al. (2012), which involves direct simulations of residuals from the models. This requires o$family$rd to be defined. Setting method = "simul2" results in a cheaper method, described in section 2.2 of Augustin et al. (2012), which requires o$family$qf to be defined.

References

Augustin, N.H., Sauleau, E.A. and Wood, S.N., 2012. On quantile quantile plots for generalized linear models. Computational Statistics & Data Analysis, 56(8), pp.2404-2409.

Examples

######## Example: simulate binomial data
library(mgcViz)
set.seed(0)
n.samp <- 400
dat <- gamSim(1,n = n.samp, dist = "binary", scale = .33)
p <- binomial()$linkinv(dat$f) ## binomial p
n <- sample(c(1, 3), n.samp, replace = TRUE) ## binomial n
dat$y <- rbinom(n, n, p)
dat$n <- n
lr.fit <- gam(y/n ~ s(x0) + s(x1) + s(x2) + s(x3)
              , family = binomial, data = dat,
              weights = n, method = "REML")
lr.fit <- getViz(lr.fit)

# Quick QQ-plot of deviance residuals
qq(lr.fit, method = "simul2")

# Same, but changing points share and type of reference list
qq(lr.fit, method = "simul2", 
       a.qqpoi = list("shape" = 1), a.ablin = list("linetype" = 2))

# Simulation based QQ-plot with reference bands 
qq(lr.fit, rep = 100, level = .9, CI = "quantile")

# Simulation based QQ-plot, Pearson resids, all simulations lines shown 
qq(lr.fit, rep = 100, CI = "none", showReps = TRUE, type = "pearson", 
       a.qqpoi = list(shape=19, size = 0.5))

### Now fit the wrong model and check
pif <- gam(y ~ s(x0) + s(x1) + s(x2) + s(x3)
           , family = poisson, data = dat, method = "REML")
pif <- getViz(pif)

qq(pif, method = "simul2")

qq(pif, rep = 100, level = .9, CI = "quantile")

qq(pif, rep = 100, type = "pearson", CI = "none", showReps = TRUE, 
               a.qqpoi = list(shape=19, size = 0.5))

######## Example: binary data model violation so gross that you see a problem 
######## on the QQ plot
y <- c(rep(1, 10), rep(0, 20), rep(1, 40), rep(0, 10), rep(1, 40), rep(0, 40))
x <- 1:160
b <- glm(y ~ x, family = binomial)
class(b) <- c("gamViz", class(b)) # Tricking qq.gamViz to use it on a glm

# Note that the next two are not necessarily similar under gross 
# model violation...
qq(b, method = "simul2")
qq(b, rep = 50, CI = "none", showReps = TRUE)

### alternative model
b <- gam(y ~ s(x, k = 5), family = binomial, method = "ML")
b <- getViz(b)

qq(b, method = "simul2")
qq(b, rep = 50, showReps = TRUE, CI = "none", shape = 19)

if (FALSE) {
########  "Big Data" example: 
set.seed(0)
n.samp <- 50000
dat <- gamSim(1,n=n.samp,dist="binary",scale=.33)
p <- binomial()$linkinv(dat$f) ## binomial p
n <- sample(c(1,3),n.samp,replace=TRUE) ## binomial n
dat$y <- rbinom(n,n,p)
dat$n <- n
lr.fit <- bam(y/n ~ s(x0) + s(x1) + s(x2) + s(x3)
              , family = binomial, data = dat,
              weights = n, method = "fREML", discrete = TRUE)
lr.fit <- getViz(lr.fit)

# Turning discretization off (on by default for large datasets).
set.seed(414) # Setting the seed because qq.gamViz is doing simulations
o <- qq(lr.fit, rep = 10, method = "simul1", CI = "normal", showReps = TRUE, 
            discrete = F, a.replin = list(alpha = 0.1))
o # This might take some time!

# Using default discretization
set.seed(414)
o <- qq(lr.fit, rep = 10, method = "simul1", CI = "normal", showReps = TRUE, 
            a.replin = list(alpha = 0.1))
o # Much faster plotting!

# Very coarse discretization
set.seed(414)
o <- qq(lr.fit, rep = 10, method = "simul1", CI = "normal", showReps = TRUE,
            ngr = 1e2, a.replin = list(alpha = 0.1), a.qqpoi = list(shape = 19))
o 

# We can also zoom in at no extra costs (most work already done by qq.gamViz)
zoom(o, xlim = c(-0.25, 0.25), showReps = TRUE, discrete = TRUE, a.replin = list(alpha = 0.2))
}