A script to produce "Size Productivity Trophic Level Charts" as described in
Froese, R., Palomares, M. L. D., Bailly, N., Coro, G., Garilao, C., Pauly, D. (2022) "A framework for the exploration of functional biodiversity".
The following code reports examples to run the script with different options. More examples can be found in the usage_example_size_productivity_trophiclevel_chart.R script.
source("size_productivity_trophiclevel_chart.R")
setwd("./")
#Default value:
#sp.classes.df = data.frame(sp.class.names = c("Myx","Pet","Hol","Ela","Cla","Act","Coe","Dip"), sp.class.codes = c(1,2,3,4,9,6,10,11))
#axes.labels = data.frame(productivity.labels<-c("High","Medium","Low","Very-low"),size.labels<-c("Small","Medium","Large","Very large"))
#input files
file = "./BioDiv_14.csv"
#example 1 - produce the chart with default labels and don't save the plot (default)
sptchart(file=file)
#example 2 - produce the chart with default labels and save the plot
sptchart(file=file,save.plot = T)
#set custom labels and codes:
sp.classes.df = data.frame(sp.class.names = c("My","Pe","Ho","El","Cl","Ac","Co","Di"), sp.class.codes = c(1,2,3,4,9,6,10,11))
axes.labels = data.frame(productivity.labels<-c("H","M","L","VL"),size.labels<-c("S","M","L","VL"))
#example 3 - produce the chart with custom class labels
sptchart(file=file,sp.classes.df=sp.classes.df)
#example 4 - produce the chart with custom labels and save the plot
sptchart(file=file,sp.classes.df=sp.classes.df,axes.labels=axes.labels,save.plot = T)
#example 5 - produce the chart with custom axes labels
sptchart(file=file,axes.labels=axes.labels)
order.age.file = "./OrderAge.csv"
#example 6 - produce the chart using custom order-age file
sptchart(file=file,order.age.file=order.age.file)
shapesToDisplay.file = "./shapesToDisplay.csv"
#example 7 - display shapes at custom locations
sptchart(file=file,shapesTodisplayFile = shapesToDisplay.file)
#example 8 - display shapes and save
sptchart(file=file,shapesTodisplayFile = shapesToDisplay.file, save.plot=T)