make clean function with compartments as arguments

instead of

```r
initial_conditions_inf <- c(
S = 1 - initial_i, E = 0, I = initial_i, R = 0, V = 0
)
```

do:
```r
initial_conditions_inf <- c(
S = 1 - initial_i,
E = 0,
I = initial_i,
R = 0,
V = 0
)
```

Search the tutorial sources for initial_conditions_inf and the compact c(...) formatting shown in the issue. Reformat the matching compartment definitions with one assignment per line, then review the rendered tutorial to confirm the examples are consistently readable.

Written by the indexing model from the issue text.