Custom sets

In addition to the pre-defined sets provided, GDSiMS features a custom parameter set section within the command-line interface (CLI) for more customised modelling work. The CLI will guide you through entering a file with parameters to setting more advanced options. You can follow our tutorial on this - Tutorial 2. Running a custom set.

Custom set runs are also available through direct interaction with the source code classes - more information in the Interacting through code section.

Parameter input file

The CLI will first ask for a parameter file, where the parameters must be listed in the order given.

An example of this parameter file is given below, with added labels.

To input the file, the CLI will ask for a filename. This may be one of three:

• An absolute filepath, e.g. C:\Users\MyUser\GeneralMetapop\params_set100.txt for Windows, home/user/GeneralMetapop/Params/params_set100.txt for Linux

• A relative filepath, relative to the build directory, e.g. ../params_set100.txt

• A filename, if the file is within the build directory, e.g. params_set100.txt

The expected directory structure of the repository is discussed in the Installation section.

Upon entering a parameter file the CLI will carry out bound and interval checks on the parameters, among other checks. If there are any errors, another file (or the same one but corrected) will be required to proceed.

The expected bounds on parameters can be found below.

Parameter	Number type	Range
num_runs	Integer	(0, inf)
max_t	Integer	(0, inf)
num_pat	Integer	(0, inf)
mu_j	Continuous	[0, 1)
mu_a	Continuous	(0, 1)
beta	Continuous	(0, inf)
theta	Continuous	(0, inf)
comp_power	Continuous	(0, inf)
min_dev	Integer	(0, inf)
gamma	Continuous	[0, 1]
xi	Continuous	[0, 1]
e	Continuous	[0, 1]
driver_start	Integer	[1, inf)
num_driver_M	Integer	[0, inf)
num_driver_sites	Integer	[0, inf)
disp_rate	Continuous	[0, 1]
max_disp	Continuous	(0, side]
psi	Continuous	[0, 1]
mu_aes	Continuous	[0, 1]
t_hide1	Integer	[1, 365]
t_hide2	Integer	[t_hide1, 365]
t_wake1	Integer	[1, 365]
t_wake2	Integer	[t_wake2, 365]
alpha0_mean	Continuous	(0, inf)
alpha0_variance	Continuous	[0, inf)
alpha1	Continuous	[0, inf)
amp	Continuous	[0, 1]
resp	Continuous	[0, inf)
rec_start	Integer	[0, inf)
rec_end	Integer	[rec_start, inf)
rec_interval_global	Integer	[1, inf)
rec_interval_local	Integer	[1, inf)
rec_sites_freq	Integer	[1, inf)
set_label	Integer	[0, inf)

() and [] denote excluding and including the bound, respectively.

Advanced options

Custom set runs on the CLI provide a submenu to set advanced options.

Multiple options can be set one after the other. If setting an option is unsuccessful (i.e. there are error messages), the option can be re-set by selecting it again.

Caution

If you exit the advanced options menu and run the program with an unsuccessful setting option, this option will maintain its default behaviour. More information in the Default behaviours section.

Equally, the advanced options can be re-set at any point for any other reasons, as long as this is prior to exiting the advanced options menu.

Note

For options requiring input files, once the advanced behaviour has been successfully set the default behaviour cannot be reset. Only new files can be provided for resets. If one of these resets fails, the program will default to the last successful attempt - if none were successful, the original default behaviour will be maintained. More information on this in the Advanced options section.