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avallecam merged 2 commits into from
Jun 26, 2025
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update installation and add rtools steps #8

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update installation and add rtools steps
avallecam Jun 26, 2025
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add install package alternative
avallecam Jun 26, 2025
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39 changes: 37 additions & 2 deletions episodes/Serofoi-tutorial.Rmd
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Expand Up @@ -315,12 +315,47 @@ The logarithm in the $log(\lambda)$ model allows to identify drastic changes in

Prior to the installation of **serofoi**, create an R project in the folder of your choice on your local machine; this in order to organize the workspace where the codes you develop during the session will be stored.

Before installing **serofoi**, it is necessary to install and configure C++ Toolchain (instructions for [windows](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows)/ [mac](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Mac)/ [linux](https://github.com/stan-dev/rstan/wiki/Configuring-C-Toolchain-for-Linux)).
Before installing **serofoi**, it is necessary to install and configure C++ Toolchain (instructions for [windows](https://cran.r-project.org/bin/windows/Rtools/)/ [mac](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Mac)/ [linux](https://github.com/stan-dev/rstan/wiki/Configuring-C-Toolchain-for-Linux)).

::::::::::::::::::::::::::::: spoiler

### how to install and configure Rtools in Windows?

Windows users will need a working installation of `Rtools` in order to build the package from source. `Rtools` is not an R package, but a software you need to download and install. We suggest you to follow:

<!-- reference [these steps](http://jtleek.com/modules/01_DataScientistToolbox/02_10_rtools/#1) -->

1. **Verify `Rtools` installation**. You can do so by using Windows search across your system. Optionally, you can use `{devtools}` running:

```r
if(!require("devtools")) install.packages("devtools")
devtools::find_rtools()
```

If the result is `FALSE`, then you should do step 2.

2. **Install `Rtools`**. Download the `Rtools` installer from <https://cran.r-project.org/bin/windows/Rtools/>. Install with default selections.

3. **Verify `Rtools` installation**. Again, we can use `{devtools}`:

```r
if(!require("devtools")) install.packages("devtools")
devtools::find_rtools()
```

:::::::::::::::::::::::::::::

After you have configured C++ Toolchain, run the following lines of code to install the package:

```{r, eval=FALSE}
if(!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/serofoi")
pak::pak("serofoi")
```

If you get an error, your can try:

```{r, eval=FALSE}
install.packages("serofoi")
```

Optionally, it is possible to modify the R configuration so that the models to be implemented run in parallel, taking advantage of the processor cores of your computer.
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