In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

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

sessionInfo()

adrientaudiere/MiscMetabar documentation built on Feb. 7, 2025, 5:47 p.m.