Choropleth example Covid rate of infection in Portugal

First, download the Portuguese district polygons shape file from this Github repo Next load it with:

using GMT, DataFrames, CSV

Pt = gmtread("C:\\programs\\compa_libs\\covid19pt\\extra\\mapas\\concelhos\\concelhos.shp");

Download and load a CSV file from same repo with rate of infection per district. Load it into a DataFrame to simplify data extraction.

incidence = CSV.read("C:\\programs\\compa_libs\\covid19pt\\data_concelhos_incidencia.csv", DataFrame);

Get the rate of incidence in number of infected per 100_000 habitants for the last reported week.

r = collect(incidence[end, 2:end]);

But the damn polygon names above are all uppercase, Ghrrr. We will have to take care of that.

ids = names(incidence)[2:end];

Each of the Pt datasets have attributes (e.g., Pt[1].attrib) and the one that is common with the names in ids is the $Pt[1].attrib["NAME_2]$ (the conselho name). But the names in dataconcelhosincidencia.csv (from which the ids are derived) and the concelhos.shp (that we read into $Pt$) do not use the same case (one is full upper case) so we need to use the $nocase=true$ below. The comparison is made inside the next call to the $polygonlevels()$ function that takes care to return the numerical vector that we need in plot's level option.

zvals = polygonlevels(Pt, ids, r, att="NAME_2", nocase=true);

Create a Colormap to paint the district polygons

C = makecpt(range=(0,1500,10), inverse=true, cmap=:oleron, hinge=240, bg=:o);

Get the date for the data being represented to use in title

date = incidence[end,1];

And finaly do the plot

plot(Pt, level=zvals, cmap=C, pen=0.5, region=(-9.75,-5.9,36.9,42.1), proj=:Mercator, title="Infected / 100.000 habitants " * date)

colorbar!(pos=(anchor=:MR,length=(12,0.6), offset=(-2.4,-4)), color=C, axes=(annot=100,), show=true)

Download a Pluto Notebook here