From b60ff200ff88edee9d9fac85ec45c6ae2d9eddb3 Mon Sep 17 00:00:00 2001 From: xec-cm Date: Thu, 3 Aug 2023 09:11:21 -0400 Subject: [PATCH] closes #91 --- .github/workflows/check-bioc.yml | 2 +- README.Rmd | 2 +- README.md | 70 ++++++++++++++++---------------- 3 files changed, 37 insertions(+), 37 deletions(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 70db23f..720d6a2 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -252,7 +252,7 @@ jobs: - name: Test coverage if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' run: | - covr::codecov() + covr::codecov(coverage = covr::package_coverage(type = "all")) shell: Rscript {0} - name: Install package diff --git a/README.Rmd b/README.Rmd index 8477636..f668e1d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,7 +18,7 @@ knitr::opts_chunk$set( [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![R-CMD-check](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/actions) -[![Codecov test coverage](https://codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar/branch/main/graph/badge.svg)](https://app.codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar?branch=main) +[![Codecov test coverage](https://codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar?branch=devel) [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](https://makeapullrequest.com) [![GitHub issues](https://img.shields.io/github/issues/MicrobialGenomics-IrsicaixaOrg/dar)](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues) [![GitHub pulls](https://img.shields.io/github/issues-pr/MicrobialGenomics-IrsicaixaOrg/dar)](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/pulls) diff --git a/README.md b/README.md index 5f46fdc..87c7911 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![R-CMD-check](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/actions) [![Codecov test -coverage](https://codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar/branch/main/graph/badge.svg)](https://app.codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar?branch=main) +coverage](https://codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/MicrobialGenomics-IrsicaixaOrg/dar?branch=devel) [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](https://makeapullrequest.com) [![GitHub @@ -73,13 +73,13 @@ rec #> #> Preporcessing steps: #> -#> ◉ step_subset_taxa() id = subset_taxa__Sad_cake -#> ◉ step_filter_taxa() id = filter_taxa__Malsouka +#> ◉ step_subset_taxa() id = subset_taxa__Milhoja +#> ◉ step_filter_taxa() id = filter_taxa__Papanași #> #> DA steps: #> -#> ◉ step_metagenomeseq() id = metagenomeseq__Moorkop -#> ◉ step_maaslin() id = maaslin__Flaugnarde +#> ◉ step_metagenomeseq() id = metagenomeseq__Schaumrolle +#> ◉ step_maaslin() id = maaslin__Punschkrapfen ## Prep recipe da_results <- prep(rec, parallel = TRUE) @@ -93,10 +93,10 @@ da_results #> #> Results: #> -#> ✔ metagenomeseq__Moorkop diff_taxa = 278 -#> ✔ maaslin__Flaugnarde diff_taxa = 205 +#> ✔ metagenomeseq__Schaumrolle diff_taxa = 236 +#> ✔ maaslin__Punschkrapfen diff_taxa = 146 #> -#> ℹ 205 taxa are present in all tested methods +#> ℹ 124 taxa are present in all tested methods ## Consensus strategy n_methods <- 2 @@ -111,47 +111,47 @@ da_results #> #> Results: #> -#> ✔ metagenomeseq__Moorkop diff_taxa = 278 -#> ✔ maaslin__Flaugnarde diff_taxa = 205 +#> ✔ metagenomeseq__Schaumrolle diff_taxa = 236 +#> ✔ maaslin__Punschkrapfen diff_taxa = 146 #> -#> ℹ 205 taxa are present in all tested methods +#> ℹ 124 taxa are present in all tested methods #> #> Bakes: #> -#> ◉ 1 -> count_cutoff: 2, weights: NULL, exclude: NULL, id: bake__Curry_puff +#> ◉ 1 -> count_cutoff: 2, weights: NULL, exclude: NULL, id: bake__Belokranjska_povitica ## Results cool(da_results) #> ℹ Bake for count_cutoff = 2 -#> # A tibble: 205 × 2 -#> taxa_id taxa -#> -#> 1 Otu_1 Methanobrevibacter_smithii -#> 2 Otu_2 Methanosphaera_stadtmanae -#> 3 Otu_10 Bifidobacterium_adolescentis -#> 4 Otu_12 Bifidobacterium_animalis -#> 5 Otu_13 Bifidobacterium_bifidum -#> 6 Otu_15 Bifidobacterium_catenulatum -#> 7 Otu_18 Bifidobacterium_longum -#> 8 Otu_19 Bifidobacterium_pseudocatenulatum -#> 9 Otu_34 Olsenella_scatoligenes -#> 10 Otu_35 Collinsella_aerofaciens -#> # … with 195 more rows +#> # A tibble: 124 × 2 +#> taxa_id taxa +#> +#> 1 Otu_63 Bacteroides_plebeius +#> 2 Otu_216 Clostridium_sp_CAG_632 +#> 3 Otu_441 Brachyspira_sp_CAG_700 +#> 4 Otu_108 Prevotella_sp_CAG_520 +#> 5 Otu_257 Butyrivibrio_sp_CAG_318 +#> 6 Otu_104 Prevotella_sp_CAG_1092 +#> 7 Otu_69 Bacteroides_sp_CAG_530 +#> 8 Otu_102 Prevotella_sp_AM42_24 +#> 9 Otu_159 Lactobacillus_ruminis +#> 10 Otu_117 Alistipes_inops +#> # ℹ 114 more rows ``` ## Contributing -- If you think you have encountered a bug, please [submit an - issue](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues). +- If you think you have encountered a bug, please [submit an + issue](https://github.com/MicrobialGenomics-IrsicaixaOrg/dar/issues). -- Either way, learn how to create and share a - [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html) - (a minimal, reproducible example), to clearly communicate about your - code. +- Either way, learn how to create and share a + [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html) + (a minimal, reproducible example), to clearly communicate about your + code. -- Working on your first Pull Request? You can learn how from this - *free* series [How to Contribute to an Open Source Project on - GitHub](https://kcd.im/pull-request) +- Working on your first Pull Request? You can learn how from this *free* + series [How to Contribute to an Open Source Project on + GitHub](https://kcd.im/pull-request) ## Code of Conduct