wplot_geog: Plotting function for displaying samples' linear discriminant...

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 for displaying samples' linear discriminant scores from wmodel.LDA compared to with the chosen modern model's centroids, and the model's discriminant scores separated according to modern study location

Description

A function which plots the samples' linear discriminant scores from wmodel.LDA, the chosen model's centroids, and the model's discriminant scores with separate symbols for the different modern study's arable fields.

Usage

wplot_geog(model, x,xlims= NULL,ticks= NULL,col1= "black",col2= "black",
col3= "black",pch1= 1,pch3= 5,xlab="Discriminant function",compact= FALSE,
priority= "descending",site= "Samples",lcol=col3, lpch=pch3, lines= TRUE,
legend= TRUE)

Arguments

model	The modern model to be plotted – either "model1", "model3" or "model3" following wmodel.LDA
x	The data frame which contains the linear discriminant scores of the anaylsised data from wmodel.LDA. Can also use linear discriminant scores from alternative sources however the column needs to be called LD1
xlims	The limits of the x axis
ticks	The location of the x axis ticks
col1	The colour of the modern model's centroids
col2	The colour of the modern model's datapoints
col3	The colour of the entered samples' datapoints
pch1	The symbol of the modern model's centroids- must be between 0 and 2
pch3	The symbol of the entered samples' datapoints
xlab	The label for the x axis
compact	Follows the beeswarm package's swarmy compact variable
priority	Follows swarmy priority regarding the method of point layout
site	Adds the name of the entered data to be shown in the legend
lcol	Colour for the entered samples in legend - use if multiple colours are used in col3
lpch	Symbol shape for the entered samples in legend - use if multiple symbols are used in pch3
lines	Adds lines from group centroid to x-axis
legend	Adds a legend to the plot

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_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 with defaults

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

##Use of model 1 -  modern data from Asturias, Spain and Haute Provence, France
#- see Bogaard et al. 2016

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

##Use of model 2 - modern data from Evvia, Greece; Asturias, Spain; Haute Provence,
#France; and oases and rain fed terraces in Morocco - see Bogaard et al. 2018

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

##Use of model 3 - modern data from Highgrove and Laxton, UK- see Bogaard et al. 2022

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


##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_geog(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",col3="purple",
pch1=1,  pch3=19,compact =FALSE, priority = "ascending")
mtext("ascending", 3,-1.5)
wplot_geog(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",col3="purple",
pch1=1,  pch3=19,compact =FALSE, priority = "descending")
mtext("descending", 3, -1.5)
wplot_geog(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",col3="purple",
pch1=1, pch3=19,compact =FALSE, priority = "density")
mtext("density",3, -1.5)
wplot_geog(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",col3="purple",
pch1=1,  pch3=19,compact =FALSE, priority = "random")
mtext("random",3,-1.5)
wplot_geog(1,data,xlims=c(-7,7),ticks=-7:7, col1="green", col2="red",col3="purple",
pch1=1,  pch3=19,compact =FALSE, priority = "none")
mtext("none",3, -1.5)

## options with compact TRUE and FALSE using ascending and descending priority

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

## options with different col and pch for different archaeobotanical sites or different phases

wplot_geog("model2", data, col3=data$Study,pch3=data$Study, legend=TRUE, site=c("Site 1",
"Site 2","Site 3"))

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