For PCA, we need to transform our AMR data first. This is what the example_isolates
data set in this package looks like:
-library(AMR)
+library(AMR)
library(dplyr)
glimpse(example_isolates)
# Rows: 2,000
# Columns: 49
-# $ date <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…
-# $ hospital_id <fct> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B, …
-# $ ward_icu <lgl> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TR…
-# $ ward_clinical <lgl> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FA…
-# $ ward_outpatient <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE…
-# $ age <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71…
-# $ gender <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M",…
-# $ patient_id <chr> "A77334", "A77334", "067927", "067927", "067927", "067…
-# $ mo <mo> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPH…
-# $ PEN <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, …
-# $ OXA <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ FLC <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, …
-# $ AMX <rsi> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …
-# $ AMC <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, …
-# $ AMP <rsi> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …
-# $ TZP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ CZO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ FEP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ CXM <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R,…
-# $ FOX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ CTX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …
-# $ CAZ <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S…
-# $ CRO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …
-# $ GEN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ TOB <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA…
-# $ AMK <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ KAN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ TMP <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R…
-# $ SXT <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, …
-# $ NIT <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ FOS <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ LNZ <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…
-# $ CIP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, …
-# $ MFX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ VAN <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S…
-# $ TEC <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…
-# $ TCY <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S…
-# $ TGC <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …
-# $ DOX <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …
-# $ ERY <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …
-# $ CLI <rsi> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, …
-# $ AZM <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …
-# $ IPM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …
-# $ MEM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ MTR <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ CHL <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ COL <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R…
-# $ MUP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
-# $ RIF <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…