centiles: Plots the centile curves for a GAMLSS object

Description

This function centiles() plots centiles curves for distributions belonging to the GAMLSS family of distributions. The function also tabulates the sample percentages below each centile curve (for comparison with the model percentages given by the argument cent.) The function centiles.fan() plots a fan-chart of the centile curves. A restriction of the functions is that it applies to models with one explanatory variable only.

Usage

centiles(obj, xvar, cent = c(0.4, 2, 10, 25, 50, 75, 90, 98, 99.6), 
         legend = TRUE, ylab = "y", xlab = "x", main = NULL, 
         main.gsub = "@", xleg = min(xvar), yleg = max(obj$y), 
         xlim = range(xvar), ylim = range(obj$y), save = FALSE, 
         plot = TRUE, points = TRUE,  pch =  15, cex = 0.5, col =  gray(0.7), 
         col.centiles = 1:length(cent) + 2, lty.centiles = 1, lwd.centiles = 1, ...)
centiles.fan(obj, xvar, cent = c(0.4, 2, 10, 25, 50, 75, 90, 98, 99.6), 
         ylab = "y", xlab = "x", main = NULL, main.gsub = "@", 
         xleg = min(xvar), yleg = max(obj$y), xlim = range(xvar), 
         ylim = range(obj$y), points = FALSE,  median = TRUE, pch =  15, 
         cex = 0.5, col =  gray(0.7),
         colors = c("cm", "gray", "rainbow", "heat", "terrain", "topo"), ...)

Value

A centile plot is produced and the sample centiles below each centile curve are printed (or saved)

Arguments

obj: a fitted gamlss object from fitting a gamlss distribution
xvar: the unique explanatory variable
cent: a vector with elements the % centile values for which the centile curves have to be evaluated
legend: whether a legend is required in the plot or not, the default is legent=TRUE
ylab: the y-variable label
xlab: the x-variable label
main: the main title here as character. If NULL the default title "centile curves using NO" (or the relevant distributions name) is shown
main.gsub: if the main.gsub (with default "@") appears in the main title then it is substituted with the default title.
xleg: position of the legend in the x-axis
yleg: position of the legend in the y-axis
xlim: the limits of the x-axis
ylim: the limits of the y-axis
save: whether to save the sample percentages or not with default equal to FALSE. In this case the sample percentages are printed but are not saved
plot: whether to plot the centiles. This option is useful for centile.split
pch: the character to be used as the default in plotting points see par
cex: size of character see par
col: plotting colour see par
col.centiles: Plotting colours for the centile curves
lty.centiles: line type for the centile curves
lwd.centiles: The line width for the centile curves
colors: the different colour schemes to be used for the fan-chart. The following are available c("cm","gray", "rainbow", "heat", "terrain", "topo"),
points: whether the data points should be plotted, default is TRUE for centiles() and FALSE for centiles.fan()
median: whether the median should be plotted (only in centiles.fan())
...: for extra arguments

Author

Mikis Stasinopoulos d.stasinopoulos@londonmet.ac.uk, Bob Rigby r.rigby@londonmet.ac.uk with contribution from Steve Ellison

Warning

This function is appropriate only when one continuous explanatory variable is fitted in the model

Details

Centiles are calculated using the fitted values in obj and xvar must correspond exactly to the predictor in obj to plot correctly.

col.centiles, lty.centiles and lwd.centiles may be vector arguments and are recycled to the length cent if necessary.

References

Rigby, R. A. and Stasinopoulos D. M. (2005). Generalized additive models for location, scale and shape,(with discussion), Appl. Statist., 54, part 3, pp 507-554.

Rigby, R. A., Stasinopoulos, D. M., Heller, G. Z., and De Bastiani, F. (2019) Distributions for modeling location, scale, and shape: Using GAMLSS in R, Chapman and Hall/CRC. An older version can be found in https://www.gamlss.com/.

Stasinopoulos D. M. Rigby R.A. (2007) Generalized additive models for location scale and shape (GAMLSS) in R. Journal of Statistical Software, Vol. 23, Issue 7, Dec 2007, https://www.jstatsoft.org/v23/i07/.

Stasinopoulos D. M., Rigby R.A., Heller G., Voudouris V., and De Bastiani F., (2017) Flexible Regression and Smoothing: Using GAMLSS in R, Chapman and Hall/CRC.

(see also https://www.gamlss.com/).

Examples

Run this code

data(abdom)
h<-gamlss(y~pb(x), sigma.formula=~pb(x), family=BCT, data=abdom) 
# default plot
centiles(h,xvar=abdom$x)
# control of colours and lines
centiles(h, xvar=abdom$x,  col.cent=c(2,3,4,5,1,5,4,3,2,1), 
              lwd.cent=c(1,1,1,1,2,1,1,1,1))
#Control line types
centiles(h, xvar=abdom$x,  col.cent=1, cent=c(.5,2.5,50,97.5,99.5), 
              lty.centiles=c(3,2,1,2,3),lwd.cent=c(1,1,2,1,1))
# control of the main title
centiles(h, xvar=abdom$x,  main="Abdominal data \n @")
# the fan-chart
centiles.fan(h,xvar=abdom$x, colors="rainbow")
rm(h)

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