wplot_phase: Function to plot samples' linear discriminant scores and...

In elizabethastroud/FIBS-R-Package: Classification of unknown cases (e.g. archaeobotanical data or other modern weed survey data) using linear discriminant analysis to understand farming regimes

Function to plot samples' linear discriminant scores and model's centroids by phase or site

Description

A function which plots the samples' linear discriminant scores from wmodel.LDA compared to the chosen modern model's group centroids as stacked graphs depending on number of grouping variables (i.e. sites or phase).

Usage

wplot_phase(model, x,
site= c("phase 1", "phase 2", "phase 3", "phase 4", "phase 5"),
g1=NULL, g2= NULL, g3=NULL, g4=NULL, g5=NULL,
gcol=c("black","black","black","black", "black"),
gpch=c(22,23,24,8,4), gbg=c("grey","grey","grey","grey", "grey"), pcolumn, compact= FALSE,
priority= "density", xlims= NULL, ylims = NULL, ticks =NULL, xlab="Discriminant function",
lines=TRUE, lcex=1)

Arguments

model	Either "model1", "model2" or "model3" - following wmodel.LDA
x	The output from wmodel.LDA, or one containing LDA scores. This should also contain a grouping variable to be used in argument pcolumn
site	The names to appear in the legend
g1	Name of phase/site group 1 in pcolumn
g2	Name of phase/site group 2 in pcolumn
g3	Name of phase/site group 3 in pcolumn
g4	Name of phase/site group 4 in pcolumn
g5	Name of phase/site group 5 in pcolumn
gcol	Symbol colour for athe entered samples' phases
gpch	Symbol shape for the entered samples' phases
gbg	Symbol infill colour if using pch 21,22,23,24 or 25
pcolumn	The column with the phases of each sample from the dataframe x
compact	Follows swarmy from the beeswarm package
priority	Follows the swarmy function relating to the method of point layout
xlims	The x axis limits
ylims	The y axis limits
ticks	The location of the x axis ticks
xlab	x axis label
lines	Adds lines from group centroid to x-axis
lcex	Size of the legend text

Author(s)

Elizabeth Stroud

See Also

wmodel.LDA, wplot_geog, wplot_basic

Examples

## Example dataset

LD1<-runif(40, min=-6.6, max=6)
Study<-sample(1:3, 40, replace=TRUE)
data<-data.frame(Study,LD1)

## If using defaults

wplot_phase( "model1", data, pcolumn= data$Study, g1=1, g2=2, g3=3,
site=c("phase 1", "phase 2", "phase 3"))

## Changes to colour and symbol type

wplot_phase( "model1", data, pcolumn= data$Study, g1=1, g2=2, g3=3,
site=c("phase 1", "phase 2", "phase 3"),gpch = c(24,4,22), gbg = c("red","black","grey"),
gcol=c("black","black","black"))

elizabethastroud/FIBS-R-Package documentation built on Sept. 26, 2024, 6:40 p.m.