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‎DESCRIPTION‎

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Package: scimo
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Title: Extra Recipes Steps for Dealing with Omics Data
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Version: 0.0.3
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Version: 0.0.3.9000
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Authors@R: c(
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person("Antoine", "BICHAT", , "[email protected]", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0001-6599-7081")),

‎NEWS.md‎

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# scimo 0.0.3.9000
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# scimo 0.0.3
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* Add a dependency on **recipes** >= 1.1 to avoid stack overflow errors with long formulas, as this issue has been resolved in this version (#2).

‎README.md‎

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<!-- badges: start -->
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![packageversion](https://img.shields.io/badge/version-0.0.3-orange.svg)
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![packageversion](https://img.shields.io/badge/version-0.0.3.9000-orange.svg)
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[![R-CMD-check](https://github.com/abichat/scimo/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abichat/scimo/actions/workflows/R-CMD-check.yaml)
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[![CRAN
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status](https://www.r-pkg.org/badges/version/scimo)](https://CRAN.R-project.org/package=scimo)
@@ -35,37 +35,37 @@ data("cheese_abundance", "cheese_taxonomy")
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cheese_abundance
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#> # A tibble: 9 × 77
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#> sample cheese rind_type asv_01 asv_02 asv_03 asv_04 asv_05 asv_06 asv_07 asv_08
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#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
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#> 1 sample… Saint… Natural 1 0 38 40 1 2 31 8
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#> 2 sample… Saint… Natural 3 4 38 61 4 4 48 14
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#> 3 sample… Saint… Natural 28 16 33 23 31 29 21 1
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#> 4 sample… Livar… Washed 0 2 1 0 5 1 0 0
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#> 5 sample… Livar… Washed 0 0 4 0 1 1 2 0
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#> 6 sample… Livar… Washed 0 1 2 0 2 1 0 0
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#> 7 sample… Epois… Washed 4 2 3 0 2 5 0 0
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#> 8 sample… Epois… Washed 0 0 0 0 0 0 0 0
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#> 9 sample… Epois… Washed 0 0 1 0 0 0 2 0
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#> # ℹ 66 more variables: asv_09 <dbl>, asv_10 <dbl>, asv_11 <dbl>, asv_12 <dbl>,
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#> # asv_13 <dbl>, asv_14 <dbl>, asv_15 <dbl>, asv_16 <dbl>, asv_17 <dbl>,
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#> # asv_18 <dbl>, asv_19 <dbl>, asv_20 <dbl>, asv_21 <dbl>, asv_22 <dbl>,
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#> # asv_23 <dbl>, asv_24 <dbl>, asv_25 <dbl>, asv_26 <dbl>, asv_27 <dbl>,
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#> # asv_28 <dbl>, asv_29 <dbl>, asv_30 <dbl>, asv_31 <dbl>, asv_32 <dbl>,
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#> # asv_33 <dbl>, asv_34 <dbl>, asv_35 <dbl>, asv_36 <dbl>, asv_37 <dbl>,
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#> # asv_38 <dbl>, asv_39 <dbl>, asv_40 <dbl>, asv_41 <dbl>, asv_42 <dbl>, …
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#> sample cheese rind_type asv_01 asv_02 asv_03 asv_04 asv_05 asv_06 asv_07 asv_08 asv_09
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#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
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#> 1 sampl… Saint… Natural 1 0 38 40 1 2 31 8 15
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#> 2 sampl… Saint… Natural 3 4 38 61 4 4 48 14 20
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#> 3 sampl… Saint… Natural 28 16 33 23 31 29 21 1 7
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#> 4 sampl… Livar… Washed 0 2 1 0 5 1 0 0 0
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#> 5 sampl… Livar… Washed 0 0 4 0 1 1 2 0 0
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#> 6 sampl… Livar… Washed 0 1 2 0 2 1 0 0 0
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#> 7 sampl… Epois… Washed 4 2 3 0 2 5 0 0 0
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#> 8 sampl… Epois… Washed 0 0 0 0 0 0 0 0 0
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#> 9 sampl… Epois… Washed 0 0 1 0 0 0 2 0 0
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#> # ℹ 65 more variables: asv_10 <dbl>, asv_11 <dbl>, asv_12 <dbl>, asv_13 <dbl>,
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#> # asv_14 <dbl>, asv_15 <dbl>, asv_16 <dbl>, asv_17 <dbl>, asv_18 <dbl>, asv_19 <dbl>,
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#> # asv_20 <dbl>, asv_21 <dbl>, asv_22 <dbl>, asv_23 <dbl>, asv_24 <dbl>, asv_25 <dbl>,
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#> # asv_26 <dbl>, asv_27 <dbl>, asv_28 <dbl>, asv_29 <dbl>, asv_30 <dbl>, asv_31 <dbl>,
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#> # asv_32 <dbl>, asv_33 <dbl>, asv_34 <dbl>, asv_35 <dbl>, asv_36 <dbl>, asv_37 <dbl>,
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#> # asv_38 <dbl>, asv_39 <dbl>, asv_40 <dbl>, asv_41 <dbl>, asv_42 <dbl>, asv_43 <dbl>,
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#> # asv_44 <dbl>, asv_45 <dbl>, asv_46 <dbl>, asv_47 <dbl>, asv_48 <dbl>, …
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glimpse(cheese_taxonomy)
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#> Rows: 74
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#> Columns: 9
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#> $ asv <chr> "asv_01", "asv_02", "asv_03", "asv_04", "asv_05", "asv_06", "asv…
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#> $ lineage <chr> "k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Dothideales|f__Dot…
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#> $ kingdom <chr> "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "…
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#> $ phylum <chr> "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascomyc…
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#> $ class <chr> "Dothideomycetes", "Eurotiomycetes", "Eurotiomycetes", "Eurotiom…
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#> $ order <chr> "Dothideales", "Eurotiales", "Eurotiales", "Eurotiales", "Euroti…
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#> $ family <chr> "Dothioraceae", "Aspergillaceae", "Aspergillaceae", "Aspergillac…
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#> $ genus <chr> "Aureobasidium", "Aspergillus", "Penicillium", "Penicillium", "P…
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#> $ species <chr> "Aureobasidium Group pullulans", "Aspergillus fumigatus", "Penic…
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#> $ asv <chr> "asv_01", "asv_02", "asv_03", "asv_04", "asv_05", "asv_06", "asv_07", …
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#> $ lineage <chr> "k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Dothideales|f__Dothiorac…
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#> $ kingdom <chr> "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi"…
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#> $ phylum <chr> "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", …
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#> $ class <chr> "Dothideomycetes", "Eurotiomycetes", "Eurotiomycetes", "Eurotiomycetes…
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#> $ order <chr> "Dothideales", "Eurotiales", "Eurotiales", "Eurotiales", "Eurotiales",…
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#> $ family <chr> "Dothioraceae", "Aspergillaceae", "Aspergillaceae", "Aspergillaceae", …
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#> $ genus <chr> "Aureobasidium", "Aspergillus", "Penicillium", "Penicillium", "Penicil…
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#> $ species <chr> "Aureobasidium Group pullulans", "Aspergillus fumigatus", "Penicillium…
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```
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``` r
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#> [1] "asv_02" "asv_03" "asv_04" "asv_05" "asv_06" "asv_07" "asv_08" "asv_09"
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#>
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#> $Debaryomycetaceae
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#> [1] "asv_10" "asv_11" "asv_12" "asv_13" "asv_14" "asv_15" "asv_16" "asv_17"
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#> [9] "asv_18" "asv_19" "asv_20" "asv_21" "asv_22"
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#> [1] "asv_10" "asv_11" "asv_12" "asv_13" "asv_14" "asv_15" "asv_16" "asv_17" "asv_18"
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#> [10] "asv_19" "asv_20" "asv_21" "asv_22"
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```
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The following recipe will
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rec
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#>
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#> ── Recipe ────────────────────────────────────────────────────────────────────────
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#> ── Recipe ──────────────────────────────────────────────────────────────────────────────
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#>
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#> ── Inputs
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#> Number of variables by role
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#> Training data contained 9 data points and no incomplete rows.
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#>
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#> ── Operations
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#> • Aggregation of: asv_01, asv_02, asv_03, asv_04, asv_05, ... | Trained
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#> • Aggregation of: asv_01, asv_02, asv_03, asv_04, asv_05, asv_06, ... | Trained
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#> • TSS normalization on: Aspergillaceae Debaryomycetaceae, ... | Trained
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#> • Kruskal filtering against cheese on: Aspergillaceae, ... | Trained
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bake(rec, new_data = NULL)
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#> # A tibble: 9 × 8
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#> sample rind_type cheese Debaryomycetaceae Dipodascaceae Saccharomycetaceae
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#> <fct> <fct> <fct> <dbl> <dbl> <dbl>
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#> 1 sample1-1 Natural Saint-Ne… 0.719 0.0684 0.113
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#> 2 sample1-2 Natural Saint-Ne… 0.715 0.0725 0.119
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#> 3 sample1-3 Natural Saint-Ne… 0.547 0.277 0.0938
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#> 4 sample2-1 Washed Livarot 0.153 0.845 0.000854
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#> 5 sample2-2 Washed Livarot 0.150 0.848 0.00106
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#> 6 sample2-3 Washed Livarot 0.160 0.837 0.00108
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#> 7 sample3-1 Washed Epoisses 0.0513 0.944 0.00327
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#> 8 sample3-2 Washed Epoisses 0.0558 0.941 0.00321
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#> 9 sample3-3 Washed Epoisses 0.0547 0.942 0.00329
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#> sample rind_type cheese Debaryomycetaceae Dipodascaceae Saccharomycetaceae
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#> <fct> <fct> <fct> <dbl> <dbl> <dbl>
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#> 1 sample1-1 Natural Saint-Nectaire 0.719 0.0684 0.113
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#> 2 sample1-2 Natural Saint-Nectaire 0.715 0.0725 0.119
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#> 3 sample1-3 Natural Saint-Nectaire 0.547 0.277 0.0938
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#> 4 sample2-1 Washed Livarot 0.153 0.845 0.000854
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#> 5 sample2-2 Washed Livarot 0.150 0.848 0.00106
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#> 6 sample2-3 Washed Livarot 0.160 0.837 0.00108
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#> 7 sample3-1 Washed Epoisses 0.0513 0.944 0.00327
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#> 8 sample3-2 Washed Epoisses 0.0558 0.941 0.00321
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#> 9 sample3-3 Washed Epoisses 0.0547 0.942 0.00329
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#> # ℹ 2 more variables: `Saccharomycetales fam Incertae sedis` <dbl>,
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#> # Trichosporonaceae <dbl>
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```

‎dev/dev_history.R‎

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file.remove("README.html")
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devtools::install(upgrade = "never")
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# devtools::build()
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# pkgdown::template_reference()
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pkgdown::check_pkgdown()

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