Design (scan) files¶

The design (or scan) file specifies which adjustable variables should be changed during a metawards calculation, and which value(s) they should be changed to.

This is a column-orientated flexible-format file, using one column per adjustable variable. Like all flexible-format files you can use commas or spaces to separate columns. The separators used in the first line will be assumed to be used for the rest of the file.

Column headers¶

You should name the variables you want to adjust in the column headers. The format of these is;

variable : Just the variable name will adjust that single variable for all copies in all demographics
demographic:variable : This will adjust the single variable in only the demographic named demographic.
variable[1] : This will adjust index 1 of the named variable in all demographics.
variable["E"] : This will adjust key E of the named variable, e.g. where the key refers to the disease stage.
demographic:variable["KEY"] : This will adjust key KEY of the named variable in the named demographic.
user.myvariable : This will adjust a custom user variable called myvariable in all demographics.
.myvariable : This will also adjust a custom user variable called myvariable in all demographic (we can drop the user to save space).
demographic:.myvariable[0] : This will adjust index 0 of the custom user variable myvariable in the demographic called demographic.

The full list of in-built parameters you can adjust are listed below;

UV:
  Adjust the Parameters.UV parameter

UV_max:
  Adjust the Parameters.UV parameter

beta:
  Adjust the Disease.beta parameter

bg_foi:
  Adjust the Parameters.bg_foi parameter

contrib_foi:
  Adjust the Disease.contrib_foi parameter

daily_imports:
  Adjust the Parameters.daily_imports parameter

dyn_dist_cutoff:
  Adjust the Parameters.dyn_dist_cutoff parameter

dyn_play_at_home:
  Adjust the Parameters.dyn_play_at_home parameter

initial_inf:
  Adjust the Parameters.initial_inf parameter

length_day:
  Adjust the Parameters.length_day parameter

play_to_work:
  Adjust the Parameters.play_to_work parameter

progress:
  Adjust the Disease.progress parameter

scale_uv:
  Adjust the Parameters.scale_uv parameter

static_play_at_home:
  Adjust the Parameters.static_play_at_home parameter

too_ill_to_move:
  Adjust the Disease.too_ill_to_move parameter

user:
  Adjust a custom user-supplied parameter, held in
  Parameters.user_params[name]. Set a user parameter
  called 'name' via 'user.name' or '.name'.

work_to_play:
  Adjust the Parameters.work_to_play parameter

In addition, you can create as many custom-user parameters to adjust as you would like.

Special columns¶

There are two special columns;

repeats : Specify the number of repeats of this row of values. This should be an integer (whole number) and gives more fine-grained control to specifying the number of repeats for different rows in a design.
output: Specify the output directory in which to place the output of the model run using this row of adjustable variables. This overrides the default output directory, which is named using the fingerprint for this set of adjustable parameters. Use this if you want to have control over where all of the output is written. Note that metawards does not allow output for multiple model runs to be written to the same file, and will append numbers (e.g. x002, x003) to any duplicated names.

Default columns¶

We highly recommend that you name the columns in your design file. If you don’t, then the default columns will be used. These are;

beta[2]  beta[3]  progress[1]  progress[2]  progress[3]

Note

These defaults came from the original C version of MetaWards, and are retained so we keep backwards compatibility with the original input files.

Column data¶

Values in each column will be interpreted using metawards.Interpret. The code will try to guess the most appropriate data type, moving through simple numbers, then isoformat dates, then number expressions (including random number), then booleans, before returning the data as a string.

You can force the type of the data using numpy-style quote characters. The type characters recognised are;

d"value" : forces value to be interpreted as a date (isoformat or fuzzy date via the Python dateparser module).
f"value" : forces value to be interpreted as a number (floating point or integer)
i"value" : forces value to be interpreted as an integer (whole number)
b"value" : forces value to be interpreted as a boolean (true or false) value. The code recognises true/false, on/off and yes/no, as well as 1/0 (all case-insensitive).
s"value" : forces values to be a string. Use this if you really want a string or want to interpret the value yourself in your plugin code.

Examples¶

beta[1]  beta[2]  beta[3]
  0.5      0.5      0.5
  0.6      0.7      0.8

Two sets of variables, setting beta[1], beta[2] and beta[3] to 0.5 in the first set, and 0.6, 0.7 and 0.8 in the second set.

beta["I1"]  beta["I2"]  beta["I3"]
# initial baseline
  0.5        0.5        0.5

# increasing infectivitiy
  0.6        0.7        0.8

Same, except using the names of the disease stages and adding comments and extra whitespace to aid legibility.

.lockdown_start    .scale_rate   repeats   output
 d"March 15 2020"      0.2         5       lockdown_march
 d"April 1 2020"       0.1         3       lockdown_april

Setting the user parameters lockdown_start and scale_rate to either March 15th 2020 / 0.2 or April 1st 2020 / 0.1. Asking for 5 repeats of the March 15 data, outputting the results to directories called lockdown_march, and 3 repeats of the April lockdown, outputting the data to lockdown_april.

Note

The first repeats will be written to lockdown_march and lockdown_april, while the remainder will be written to numbered directories, e.g. lockdown_marchx002 etc.

beta[2], beta[3], progress[1], progress[2], progress[3]
 0.95,   0.95,     0.19,        0.91,         0.91
 0.90,   0.93,     0.18,        0.92,         0.90

Named columns, using comma separators, and adding extra spaces for improved legibility.