Merge pull request LebeerLab#1 from LebeerLab/dev

Refactoring package
justicengom · Oct 13, 2023 · 8d0a697 · 8d0a697
2 parents b64fe58 + 533488b
commit 8d0a697
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,3 +2,6 @@
 ^\.Rproj\.user$
 ^\.github$
 ^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -6,7 +6,7 @@
 # usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches: [main, master, feature/unit-testing]
+    branches: [main, master]
   pull_request:
     branches: [main, master]
   workflow_dispatch:
@@ -31,7 +31,7 @@ jobs:
           # use 4.1 to check with rtools40's older compiler
           - {os: windows-latest, r: '4.1'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
           - {os: ubuntu-latest,   r: 'oldrel-2'}
@@ -56,7 +56,18 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+              any::rcmdcheck
+              any::plotly
+              any::vdiffr
+              any::compositions
+              any::MCL
+              any::Matrix
+              any::umap
+              any::Rtsne
+              bioc::dada2
+              bioc::phyloseq
+              github::zdk123/SpiecEasi
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -3,8 +3,6 @@
 on:
   push:
     branches: [main, master]
-  pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -2,9 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, feature/unit-testing]
-  pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: test-coverage
 
@@ -23,7 +21,15 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: |
+                any::covr
+                any::plotly
+                any::vdiffr
+                any::compositions
+                any::umap
+                any::Rtsne
+                bioc::dada2
+                bioc::phyloseq
           needs: coverage
 
       - name: Test coverage

diff --git a/.gitignore b/.gitignore
@@ -7,5 +7,7 @@ doc
 informal_tests.R
 notes.md
 test
-tidyamplicons.Rproj
+tidytacos.Rproj
 wiki
+docs
+pkgdown
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,19 +1,21 @@
 Type: Package
-Package: tidyamplicons
-Title: Functions to Manipulate and Visualize Amplicon Abundance Data
+Package: tidytacos
+Title: Manipulate Taxonomic Composition Data of Microbial Communities
 Version: 0.2.2
-Authors@R: 
-    person("Stijn", "Wittouck", , "stijn.wittouck@uantwerpen.be", role = c("aut", "cre"))
-Description: A toolkit for processing and visualizing amplicon abundance
-    data, based on the tidyverse framework.
+Authors@R: c(
+    person("Stijn", "Wittouck", , "stijn.wittouck@uantwerpen.be", role = c("aut", "cre")),
+    person("Tim", "Van Rillaer", , "tim.vanrillaer@uantwerpen.be", role = c("aut")),
+    person("Wenke", "Smets", , "wenke.smets@uantwerpen.be", role = c("aut")),
+    person("Sarah", "Lebeer", "sarah.lebeer@uantwerpen.be", role = c("fnd")))
+Description: A toolkit for processing and visualizing taxonomic composition data
+    of microbial communities, based on the tidyverse framework.
 License: GPL-3
 Depends: R (>= 3.6.0)
 Imports:
     dplyr,
     forcats,
     ggplot2,
     magrittr,
-    plotly,
     purrr,
     readr,
     rlang (>= 0.4.11),
@@ -23,13 +25,16 @@ Imports:
     vegan
 Suggests: 
     covr,
+    compositions,
     vdiffr,
     dada2,
+    ggVennDiagram,
     knitr,
     phyloseq,
+    plotly,
     rmarkdown,
     roxygen2,
-    testthat (>= 3.0.0)
+    testthat (>= 3.1.9)
 VignetteBuilder: 
     knitr
 Encoding: UTF-8

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,95 +3,85 @@
 export("%>%")
 export(":=")
 export(.data)
-export(abundances)
-export(abundances_matrix)
+export(add_absolute_abundance)
 export(add_alphas)
-export(add_cluster)
 export(add_codifab)
 export(add_copca)
-export(add_diversity_measures)
+export(add_density)
+export(add_eigentaxa)
 export(add_jervis_bardy)
-export(add_lib_size)
 export(add_logratios)
-export(add_max_rel_abundance)
 export(add_mean_rel_abundances)
 export(add_occurrences)
-export(add_pcoa)
-export(add_presence_counts)
+export(add_ord)
 export(add_rel_abundance)
-export(add_rel_occurrence)
+export(add_sample_cluster)
 export(add_sample_clustered)
 export(add_sample_tibble)
 export(add_spike_ratio)
+export(add_taxon_cluster)
 export(add_taxon_name)
 export(add_taxon_name_color)
 export(add_taxon_tibble)
-export(add_total_rel_abundance)
+export(add_total_absolute_abundance)
+export(add_total_count)
+export(add_total_density)
 export(aggregate_samples)
 export(aggregate_taxa)
-export(as_abundances)
-export(as_abundances_matrix)
+export(as_counts)
+export(as_counts_matrix)
 export(as_label)
 export(as_name)
 export(as_phyloseq)
-export(as_tidyamplicons)
-export(bar_plot)
-export(bar_plot_ly)
 export(betas)
-export(change_id_samples)
-export(change_id_taxa)
 export(classify_taxa)
+export(clr_transform_counts)
+export(cluster_sparcc)
 export(codifab_plot)
+export(counts)
+export(counts_matrix)
 export(create_test_ta)
-export(create_tidyamplicons)
+export(create_tidytacos)
 export(enquo)
 export(enquos)
 export(everything)
-export(filter_abundances)
+export(filter_counts)
 export(filter_samples)
+export(filter_sparcc)
 export(filter_taxa)
-export(get_abundances_extended)
-export(get_bar_plot)
-export(get_betas)
-export(get_history_plot)
-export(get_numbers)
-export(get_rel_abundance_matrix)
-export(history_plot)
-export(make_tidyamplicons)
+export(from_dada)
+export(from_phyloseq)
+export(make_tidytacos)
 export(mean_rel_abundances)
-export(merge_samples)
-export(merge_taxa)
-export(merge_tidyamplicons)
-export(mutate_abundances)
+export(merge_tidytacos)
+export(mutate_counts)
 export(mutate_samples)
 export(mutate_taxa)
-export(numbers)
 export(occurrences)
-export(pcoa_plot_ly)
 export(perform_adonis)
-export(process_abundance_selection)
-export(process_sample_selection)
-export(process_taxon_selection)
 export(rank_names)
 export(rarefy)
-export(read_tidyamplicons)
+export(read_tidytacos)
+export(rel_abundance_matrix)
 export(remove_empty_samples)
-export(report_numbers)
 export(reset_ids)
-export(sample_plot)
 export(samples)
-export(select_abundances)
+export(select_counts)
 export(select_samples)
 export(select_taxa)
 export(set_rank_names)
+export(sparcc)
+export(tacoplot_ord)
+export(tacoplot_ord_ly)
+export(tacoplot_stack)
+export(tacoplot_stack_ly)
+export(tacoplot_venn)
+export(tacoplot_zoom)
+export(tacosum)
 export(taxa)
-export(taxon_counts_in_conditions)
-export(tidy_phyloseq)
+export(taxonlist_per_condition)
 export(trim_asvs)
-export(update_id_names)
-export(update_lib_sizes)
-export(update_tidyamplicons)
-export(write_tidyamplicons)
+export(write_tidytacos)
 import(dplyr)
 import(ggplot2)
 import(stringr)
@@ -106,6 +96,15 @@ importFrom(rlang,as_label)
 importFrom(rlang,as_name)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
+importFrom(stats,as.formula)
+importFrom(stats,cor.test)
+importFrom(stats,cutree)
+importFrom(stats,fisher.test)
+importFrom(stats,hclust)
+importFrom(stats,median)
+importFrom(stats,na.omit)
+importFrom(stats,p.adjust)
+importFrom(stats,prcomp)
+importFrom(stats,t.test)
+importFrom(stats,wilcox.test)
 importFrom(tibble,tibble)
-importFrom(plotly,layout)
-importFrom(plotly,plot_ly)