wplot_basic: Plotting function to display the linear discriminant scores...

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

Plotting function to display the linear discriminant scores from wmodel.LDA against the functional ecological model centroids and linear discriminant scores

Description

A function which plots the linear discriminant scores from wmodel.LDA against the functional ecological model centroids and linear discriminant scores

Usage

wplot_basic (model, x, xlims= NULL,ticks = NULL,col1 = "black",col2 = "black",
col3 = "black", pch1 = 1, pch2 = 2, pch3 = 0, xlab="Discriminant function",
compact =  FALSE, priority = "density",
lines = TRUE, site = "Samples", lcol=col3, lpch=pch3,legend = "split")

Arguments

model	The modern model to be plotted – either "model1", "model2", or "model3" - use the model against which the samples have a been classified against, using wmodel.LDA.
x	The data frame which contains the linear discriminant scores of the anaylsised data - if using data from a source other than wmodel.LDA, column needs to be called LD1
xlims	The limits of the x axis
ticks	The location of the x axis ticks along the x axis
col1	The colour of the modern model's centroids
col2	The colour of the modern model's datapoints
col3	The colour of the archaeobotanical datapoints
pch1	The symbol of the modern model's centroids - must be between 0 and 2
pch2	The symbol of the modern model's datapoints - must be between 0 and 2
pch3	The symbol of entered samples datapoints
xlab	Label on the x axis, default is "Discriminant function"
compact	Follows swarmy from the beeswarm package
priority	Follows the swarmy function relating to the method of point layout
lines	Adds lines from group centroid to x-axis
site	Add labels in the legend for the archaeobotanical data
lcol	Colour for archaeobotanical samples in legend - use if multiple colours are used in col3
lpch	Symbol shape for entered samples in legend - use if multiple symbols are used in pch3
legend	Adds a legend showing the symbols used to denote group centroids and entered samples (x). Options are "right" (located on the right- hand side), "left" (located on the left-hand side of the graph), and "split" (located on the right-hand side, with labels aligning with the graphed data)

Author(s)

Elizabeth Stroud

References

model 1 - see Bogaard, A., Hodgson, J., Nitsch, E., Jones, G., Styring, A., Diffey, C., Pouncett, J., Herbig, C., Charles, M., Ertuğ, F., Tugay, O. Filipović, D. and Fraser, R. (2016) 'Combining functional weed ecology and crop stable isotope ratios to identify cultivation intensity: a comparison of cereal production regimes in Haute Provence, France and Asturias, Spain' Vegetation History and Archaeobotany 25, 57-73

model 2 - see Bogaard, A., Styring, A., Ater, M., Hmimsa, Y., Green, L., Stroud, E., Whitlam, J., Diffey, C., Nitsch, E., Charles, M., Jones, G. and Hodgson, J.2018 'From traditional farming in Morocco to early urban agroecology in northern Mesopotamia: combining present-day arable weed surveys and crop isotope analysis to reconstruct past agrosystems in (semi-)arid regions' Environmental Archaeology 23, 303-322

model 3 - see Bogaard, A., Hodgson, J., Kropp, C., McKerracher, M. and Stroud, E. (2022). ‘Lessons from Laxton, Highgrove and Lorsch: Building arable weed-based models for the investigation of early medieval agriculture in England’, in M. McKerracher and H. Hamerow (eds) New Perspectives on the Medieval ‘Agricultural Revolution’: Crop, Stock and Furrow (Liverpool: Liverpool University Press).

See Also

wmodel.LDA, wplot_phase, wplot_geog

Examples

##Example dataset

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

##Usage with defaults

wplot_basic("model1", data)
wplot_basic("model2", data)
wplot_basic("model3", data)

## Use of model 1 - modern data from Asturias, Spain and Haute Provence, France
#(Bogaard \emph{et al.} 2016)

wplot_basic("model1",data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple",pch1=1, pch2=2, pch3=19, compact =FALSE, priority = "ascending", lines=TRUE,
site="example")

##Use of model2 - modern data from Evvia, Greece; Asturias, Spain; Haute Provence,
#France; and oases and rainfed terraces in Morocco (Bogaard \emph{et al.} 2018)

wplot_basic("model2", data, xlims=c(-7,7),ticks=-7:7, col1="green",  col2="red",
col3="purple",pch1=1, pch2=2,pch3=19, compact =FALSE, priority = "ascending", lines=TRUE,
site="example")

##Use of model3 - modern data from Highgrove and Laxton,UK -see Bogaard \emph{et al.} 2022

wplot_basic("model3", data, xlims=c(-7,7),ticks=-7:7, col1="green",  col2="red",
col3="purple",pch1=1,pch2=2, pch3=19, compact =FALSE, priority = "ascending", lines=TRUE,
site="example")

## Options with different colours and symbols for different archaeological sites

wplot_basic("model1", data, col3=data$Study,pch3=data$Study, site=c("Site 1",
"Site 2","Site 3"))

##Different priority options using "ascending", "descending", "density", "random", "none"

par(mfrow=c(3,2),
    oma=c(0,0,0,0),
    mar=c(0,0,0,0))
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1,pch2=2, pch3=19, compact =FALSE, priority = "ascending")
mtext("ascending", 3,-1.5)
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1,pch2=2, pch3=19, compact =FALSE, priority = "descending")
mtext("descending", 3, -1.5)
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1, pch2=2, pch3=19, compact =FALSE, priority = "density")
mtext("density",3, -1.5)
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1, pch2=2, pch3=19, compact =FALSE, priority = "random")
mtext("random",3,-1.5)
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1, pch2=2, pch3=19, compact =FALSE, priority = "none")
mtext("none",3, -1.5)

## Grpah options using compact TRUE and FALSE as well as ascending and descending priority

par(mfrow=c(2,2),
    oma=c(0,0,0,0),
    mar=c(0,0,0,0))
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1, pch2=2, pch3=19, compact =FALSE, priority = "ascending")
mtext("ascending, TRUE", 3,-1.5)
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1, pch2=2, pch3=19, compact =TRUE, priority = "ascending")
mtext("ascending, FALSE", 3,-1.5)
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1, pch2=2, pch3=19, compact =FALSE, priority = "descending")
mtext("descending, TRUE", 3,-1.5)
wplot_basic(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",
col3="purple", pch1=1, pch2=2, pch3=19, compact =TRUE, priority = "descending")
mtext("descending, FALSE", 3,-1.5)

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