SCGLR (version 1.2)

plot.SCGLR: SCGLR generic plot

Description

SCGLR generic plot

Usage

## S3 method for class 'SCGLR':
plot(x, ..., style = "simple", threshold = 0.8,
  plane = c(1, 2), factor = NULL, predictors = NULL, covariates = NULL,
  label.offset = 0.01, label.auto = T, label.size = 1, expand = 1)

Arguments

x

an object from SCGLR class.

...

optional arguments.

style

describes which plot will be drawn. Style "simple" : correlation plot, "covariates" (to add covariates arrows), "circle" (to add the unit circle), "observations" (to add observations), "threshold" (to select covariates whose sum of square correlat

threshold

a numeric value. All covariates whose sum of square correlations with the two components of the plane lower than this threshold will be ignored.

plane

a size-2 vector (or comma separated string) indicating which components are plotted (eg: c(1,2) or "1,2").

factor

factor to show (default to first one).

predictors

a vector of character to select the linear predictors displayed.

covariates

a vector of character to select the covariates displayed.

label.offset

offset by which labels should be moved from tip of arrows.

label.auto

whether or not the labels should be rotated according to vector angle.

label.size

relative size for labels (fine tuning).

expand

expand factor for windows size, for example to make room for clipped labels.

Value

• an object of class ggplot.

Examples

library(SCGLR)

# load sample data
data(genus)

# get variable names from dataset
n <- names(genus)
ny <- n[grep("^gen",n)]    # Y <- names that begins with "gen"
nx <- n[-grep("^gen",n)]   # X <- remaining names

# remove "geology" and "surface" from nx
# as surface is offset and we want to use geology as additional covariate
nx <-nx[!nx%in%c("geology","surface")]

# build multivariate formula
# we also add "lat*lon" as computed covariate
form <- multivariateFormula(ny,c(nx,"I(lat*lon)"),c("geology"))

# define family
fam <- rep("poisson",length(ny))

genus.scglr <- scglr(formula=form,data = genus,family=fam, K=4,
 offset=genus$surface)

summary(genus.scglr)

barplot(genus.scglr)

plot(genus.scglr)

plot(genus.scglr,style="circle,cov,predictors,fact")

pairs(genus.scglr)