Output

The main output file is called vectri.nc which is found in the run directory (unless you chose to rename it with the -o option).

The file is in standard netcdf format and you can use two commands to examine its content ncview and ncdump.

ncdump outputs the entire contents of a file, perhaps a little more than you bargained for, so use the useful option -h to examined the file header. The command lets us know the dimensions of the output, gives a list of the model output variables, as well as their metadata.

Lastly, but certainly not least, the dump provides a list of all the model run global attributes. Here you find stored all the command used to run the model, the exact github tag release used so you can reproduce the code later, and all of the run parameters (VERY USEFUL!). Most of these can be set by the user (see next section), so it is very useful to have a record inside the file! We could dump a individual variable using the ncdump -v variable command, but it is also possible to graphically interrogate the file using ncview.

Using the command ncview ./output/vectri.nc launches the graphical viewer. There is a panel containing a list of variables. Clicking on one of these variables launches a display window (Fig. ). If you conducted a gridded regional integration then you will get a map of the output, otherwise you will get a line graph for a station integration

Figure: An example ncview window showing vectri output

The input variables of population, temperature and rainfall are stored in the file.

Table: The Vectri output (some of these are optional and switched off my default)

name	definition	units
population	population density	km$^{-2}$
rain	rainfall	mm day$^{-1}$
temp	temperature	deg C
water_frac	fraction of grid box covered by pond breeding sites
vector	mosquito density
larvae	larvae density
larvae_biomass	larvae biomass	mg m$^{-2}$
PRd	proportion of population with detectable malaria (day 10+)
hbr	human bite rate	number person$^{-1}$ day$^{-1}$
cspr	Circum sporozoite protein ratio (fraction eir/hbr)
eir	entomological inoculation rate (number of infectious bites)	number person$^{-1}$ day$^{-1}$
vecthostratio	ratio of mosquitoes to people
cases	Number of clinical cases	fraction
immunity	Proportion of population with full clinical immunity	fraction