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2026-03-20 16:11:30 +00:00
parent ba003f3e23
commit 3560dfd611
115 changed files with 820 additions and 779 deletions
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11
articles/PCA.md
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@@ -78,9 +78,10 @@ resistance_data <- example_isolates %>%
order, genus, AMC, CXM, CTX,
CAZ, GEN, TOB, TMP, SXT
) # and select only relevant columns
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus
#> considers the 'I' category susceptible. Set the `guideline` argument or the
#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::AMR-options`).
#> ℹ This message will be shown once per session.
head(resistance_data)
@@ -104,8 +105,8 @@ variables, so we now only need to do:
``` r
pca_result <- pca(resistance_data)
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT",
#> "TMP", and "TOB". Total observations available: 7.
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP",
#> and "TOB". Total observations available: 7.
```
The result can be reviewed with the good old