https://github.com/kklot/endtb
TB models in TMB
https://github.com/kklot/endtb
epidemic modelling simulation tb tmb tuberculosis
Last synced: 15 days ago
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TB models in TMB
- Host: GitHub
- URL: https://github.com/kklot/endtb
- Owner: kklot
- License: other
- Created: 2023-04-11T20:03:25.000Z (about 2 years ago)
- Default Branch: master
- Last Pushed: 2023-06-28T21:26:53.000Z (almost 2 years ago)
- Last Synced: 2025-02-16T03:29:23.550Z (2 months ago)
- Topics: epidemic, modelling, simulation, tb, tmb, tuberculosis
- Language: R
- Homepage:
- Size: 399 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# EndTB
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
The goal of EndTB is to provide a convinient set of established TB models for
the simulation, estimation, and projection of Tuberculosis Epidemic.
Moreover
- the models are implemented in C++ which provides fast simulations.
- the models are called within the [TMB
framework](https://kaskr.github.io/adcomp/Introduction.html), allowing advanced
and fast parameter estimation with emprical Bayes approach.
## Installation
You can install the development version of EndTB like so:
```{r eval=FALSE}
remotes::install_github('kklot/EndTB')
```
Documents of the package and functions can be view as normal R's documentation
or online at [EndTB.](https://kklot.github.io/EndTB)
## Example
This is a basic example which shows you how to start a model:
```{r}
library(EndTB)
TB <- TBM$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