Rules.Rmd

---
title: "Rules"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Rules}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

# Rules for the package development

## Documentation

- Always indicate required params `(required)`
- Indicate default values only when (i) a set of values is possible [e.g `"bray"` for the parameter `method` in `vegan::vegdist()`] or (ii) when this value is well thought out and a good default value for most users [e.g. the number of permutation or processors, or the level of identity to cluster at 97%]. 
- Indicate the type for *logical* and *integer* params.
- Homogenize the params names across function.
- Prefer ASVs to OTUs denomination, even thought both are almost interchangeable in the MiscMetabar package. 

## Lifecycle 

- **Experimental**: First status for a function
- **Maturing**: Some tests and/or analyses make stronger these functions
- **Stable**: Good level of confidence

## Tests and examples

### Special cases of external softwares

Some examples and test required the installation of external softwares. I used MiscMetabar internal functions (such as [is_vsearch_installed()]) to conditionnaly test (`if(is_vsearch_installed()){...test...}`) and run examples `#' @examplesIf is_vsearch_installed()`.

### Special case of CRAN

I use `\donttest{}` for some long examples (in roxygen documentation) and `testthat::skip_on_cran()` in long test.

### Special case of windows

Some tests and examples are not tested on windows. I used `testthat::skip_on_os("windows")` inside test and `#' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"` in examples (roxygen documentation). Here is a list of functions with some limitations or not working at all on windows OS: 

- `build_phytree_pq()`
- `count_seq()`
- `cutadapt_remove_primers()`
- `krona()`
- `merge_krona()`
- `multipatt_pq()`
- `plot_tsne_pq()`
- `rotl_pq()`
- `save_pq()`
- `tax_datatable()`
- `track_wkflow()`
- `track_wkflow_samples()` 
- `tsne_pq()`
- `venn_pq()`

# Session information

```{r}
sessionInfo()
```