Description Usage Arguments Value Author(s) References See Also Examples
View source: R/FUNCTION_kobePlot.r
Plot 4 areas of risk in relation to a given overall threshold
1 2 3 4 5 |
dta |
data.frame containing factor to be plotted, mean x and y risk values and standard deviation or standard error (optional) |
xNam |
name of column containing information of x axis to be plotted. Defaults to 'mean_effort' |
yNam |
name of column containing information of y axis to be plotted. Defaults to 'mean_effort' |
gp |
grouping factor. Defaults to 'Spp' |
xSdUp |
name of column containing information of SD or SE upper value of x axis to be plotted as an errorbar. Defaults to 0 |
xSdLow |
name of column containing information of SD or SE lower value of x axis to be plotted as an errorbar. Defaults to 0 |
ySdUp |
name of column containing information of SD or SE upper value of y axis to be plotted as an errorbar. Defaults to 0 |
ySdLow |
name of column containing information of SD or SE lower value of y axis to be plotted as an errorbar. Defaults to 0 |
v |
vector(x,y) of risk threshold. x: x axis threshold; y: yaxis threshold |
colPlt |
Colour vector to colour geom_points. Defaults to Species colour as in paper (See References). NULL returns automatically coloured points |
gline |
Logical. Connect points by a line? TRUE draws a geom_path connecting the plotted points. Default to FALSE. |
Kobe plot with 4 risk areas: green: Low effort and overlap risk; yellow: either overlap or effort with high risk, but low for the other variable. red: high effort and overlap risk
Marisa Vedor, Ivo da Costa, Nuno Queiroz
Adapted from https://gist.github.com/jcquiroz/2695825
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | # Read Species data
dta <- data.frame('Spp' = factor(c('PGL', 'IOX', 'CCA', 'GCU')),
'mean_effort' = c(1e-5, 0.5e-5, 0.8e-5, 0.1e-5),
'mean_overlap' = c(70,65,50,10),
"upSD_effort" = c(1e-5, 0.5e-5, 0.8e-5, 0.1e-5) + 0.1e-5
"lowSD_effort" = c(1e-5, 0.5e-5, 0.8e-5, 0.1e-5) - 0.1e-5
"upSD_overlap" = c(70,65,50,10) + 10
"lowSD_effort" = c(70,65,50,10) - 10
)
# Read overall risk
v <- c(mean(dta$mean_effort), mean(dta$mean_overlap))
#### Save kobe plot ####
print(kobePlot(dta = dta, xNam = 'mean_effort', yNam = 'mean_overlap', gp = 'Spp',
xSdUp = "upSD_effort", xSdLow = "lowSD_effort",
ySdUp = "upSD_overlap", ySdLow = "lowSD_effort",
v = v))
ggsave(paste0('Fig3_', rg,'.pdf'), paper = 'a4r',
width = 250, height = 150, units = 'mm')
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