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flepimop patch documenation edits
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Stronger and clearer wording suggested by @saraloo.
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TimothyWillard committed Dec 11, 2024
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Expand Up @@ -20,19 +20,19 @@ You should see an assortment of yml files as a result of that `ls` command.

## Usage

If you run
If you run:

```bash
flepimop simulate config_sample_2pop.yml
```

you'll get a basic foward simulation of this example model. However, you might also note there are several `*_part.yml` files, corresponding to partial configs. You can `simulate` using the combination of multiple configs with, for example:
You'll get a basic forward simulation of this example model. However, you might also note there are several `*_part.yml` files, corresponding to partial configs. You can `simulate` using the combination of multiple configs with, for example:

```bash
flepimop simulate config_sample_2pop.yml config_sample_2pop_outcomes_part.yml
```

if want to create a combined configuration (e.g. to check what the combined configuration is), you can use the `patch` command:
While simulate can run your patched configuration, we also suggest you check your configuration file using the patch command:

```bash
flepimop patch config_sample_2pop.yml config_sample_2pop_outcomes_part.yml > config_new.yml
Expand All @@ -43,6 +43,6 @@ You may provide an arbitrary number of separate configuration files to combine t

## Caveats

At this time, only `simulate` supports multiple configuration files. Also, the patching operation is fairly crude: if multiple configuration files specify the same option, this will yield an error.
At this time, only simulate directly supports multiple configuration files, and our current patching capabilities only allow for the addition of new sections as given in our tutorials. This is helpful for building models piece-by-piece from a simple compartmental forward simulation, to including outcome probabilities, and finally, adding modifier sections. If multiple configuration files specify the same higher level configuration chunks (e.g., seir, outcomes), this will yield an error.

We are expanding coverage of this capability to other flepimop actions, e.g. inference, and are exploring options for smarter patching.

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