README.Rmd

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# EndTB 

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The goal of EndTB is to provide a convinient set of established TB models for
the simulation, estimation, and projection of Tuberculosis Epidemic.

Moreover

- the models are implemented in C++ which provides fast simulations.
- the models are called within the [TMB
  framework](https://kaskr.github.io/adcomp/Introduction.html), allowing advanced
  and fast parameter estimation with emprical Bayes approach.

## Installation

You can install the development version of EndTB like so:

```{r eval=FALSE}
remotes::install_github('kklot/EndTB')
```

Documents of the package and functions can be view as normal R's documentation
or online at [EndTB.](https://kklot.github.io/EndTB)

## Example

This is a basic example which shows you how to start a model:

```{r}
library(EndTB)
TB <- TBM$new(c(sigma = 2))
```

where the default parameters $\sigma$ was replaced with 2.

Steady-state of the model without treatments and no population growth
for that set of parameters can be ploted with.

```{r plot}
TB$plot()
```

List of states to be plotted can be supplied into the arguments of the `plot`
function above. 

Further details can be read in **References** in the top navigation. For
example, [the
documentation of `plot`](https://kklot.github.io/EndTB/reference/TBM.html#method-plot-). 

Check out model's parameters and states for Moldova model.

```{r para}
EndTB:::states_moldova
EndTB:::pars_moldova
```

## TODO

- [x] 1st revision of the WHO's model (and currently the only)
- [ ] Revise model to Argentina data
- [ ] Add fitting example
- [ ] Add other model variations