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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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14
vignettes/PCA.Rmd
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@@ -39,12 +39,16 @@ glimpse(example_isolates)
Now to transform this to a data set with only resistance percentages per taxonomic order and genus:
```{r, warning = FALSE}
resistance_data <- example_isolates %>%
group_by(order = mo_order(mo), # group on anything, like order
genus = mo_genus(mo)) %>% # and genus as we do here
resistance_data <- example_isolates %>%
group_by(
order = mo_order(mo), # group on anything, like order
genus = mo_genus(mo)
) %>% # and genus as we do here
summarise_if(is.rsi, resistance) %>% # then get resistance of all drugs
select(order, genus, AMC, CXM, CTX,
CAZ, GEN, TOB, TMP, SXT) # and select only relevant columns
select(
order, genus, AMC, CXM, CTX,
CAZ, GEN, TOB, TMP, SXT
) # and select only relevant columns
head(resistance_data)
```