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reference/antibiogram.md
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@@ -602,7 +602,7 @@ antibiogram(example_isolates,
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 10 × 7
#> # An antibiogram: 10 × 7
#> # Type: Non-WISCA with 95% CI
#> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
@@ -617,7 +617,7 @@ antibiogram(example_isolates,
#> 9 S. hominis NA 92% (84-9… NA NA NA 85% (74-9…
#> 10 S. pneumoniae 0% (0-3%,N… 0% (0-3%,… NA 0% (0-3%… NA 0% (0-3%,…
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
antibiogram(example_isolates,
antimicrobials = aminoglycosides(),
@@ -626,14 +626,14 @@ antibiogram(example_isolates,
)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> # An Antibiogram: 2 × 5
#> # An antibiogram: 2 × 5
#> # Type: Non-WISCA with 95% CI
#> Pathogen J01GB01 J01GB03 J01GB04 J01GB06
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Gram-negative 96% (94-97%,N=686) 96% (95-98%,N=684) 0% (0-10%,N=35) 98% (96-…
#> 2 Gram-positive 34% (31-38%,N=665) 63% (60-66%,N=1170) 0% (0-1%,N=436) 0% (0-1%…
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
antibiogram(example_isolates,
antimicrobials = carbapenems(),
@@ -641,7 +641,7 @@ antibiogram(example_isolates,
mo_transform = "name"
)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 5 × 3
#> # An antibiogram: 5 × 3
#> # Type: Non-WISCA with 95% CI
#> Pathogen Imipenem Meropenem
#> <chr> <chr> <chr>
@@ -651,7 +651,7 @@ antibiogram(example_isolates,
#> 4 Klebsiella pneumoniae 100% (93-100%,N=51) 100% (93-100%,N…
#> 5 Proteus mirabilis 94% (79-99%,N=32) NA
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
# Combined antibiogram -------------------------------------------------
@@ -661,7 +661,7 @@ antibiogram(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
mo_transform = "gramstain"
)
#> # An Antibiogram: 2 × 4
#> # An antibiogram: 2 × 4
#> # Type: Non-WISCA with 95% CI
#> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³
#> <chr> <chr> <chr> <chr>
@@ -671,7 +671,7 @@ antibiogram(example_isolates,
#> # ²​`Piperacillin/tazobactam + Gentamicin`,
#> # ³​`Piperacillin/tazobactam + Tobramycin`
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
# you can use any antimicrobial selector with `+` too:
antibiogram(example_isolates,
@@ -679,7 +679,7 @@ antibiogram(example_isolates,
mo_transform = "gramstain"
)
#> ℹ For `ureidopenicillins()` using column TZP (piperacillin/tazobactam)
#> # An Antibiogram: 2 × 4
#> # An antibiogram: 2 × 4
#> # Type: Non-WISCA with 95% CI
#> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³
#> <chr> <chr> <chr> <chr>
@@ -689,7 +689,7 @@ antibiogram(example_isolates,
#> # ²​`Piperacillin/tazobactam + Gentamicin`,
#> # ³​`Piperacillin/tazobactam + Tobramycin`
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
# names of antimicrobials do not need to resemble columns exactly:
antibiogram(example_isolates,
@@ -698,14 +698,14 @@ antibiogram(example_isolates,
ab_transform = "name",
sep = " & "
)
#> # An Antibiogram: 2 × 3
#> # An antibiogram: 2 × 3
#> # Type: Non-WISCA with 95% CI
#> Pathogen Ciprofloxacin `Ciprofloxacin & Gentamicin`
#> <chr> <chr> <chr>
#> 1 Gram-negative 91% (88-93%,N=684) 99% (97-99%,N=694)
#> 2 Gram-positive 77% (74-80%,N=724) 93% (91-94%,N=847)
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
# Syndromic antibiogram ------------------------------------------------
@@ -718,7 +718,7 @@ antibiogram(example_isolates,
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 14 × 8
#> # An antibiogram: 14 × 8
#> # Type: Non-WISCA with 95% CI
#> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
@@ -738,7 +738,7 @@ antibiogram(example_isolates,
#> 14 ICU S. pneumo… 0% (0-1… 0% (0-12%… NA 0% (0-12… NA
#> # ℹ 1 more variable: Tobramycin <chr>
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
# now define a data set with only E. coli
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
@@ -756,14 +756,14 @@ antibiogram(ex1,
)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> # An Antibiogram: 2 × 5
#> # An antibiogram: 2 × 5
#> # Type: Non-WISCA with 95% CI
#> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina
#> <chr> <chr> <chr> <chr> <chr>
#> 1 No UCI E. coli 100% (97-100%,N=119) 98% (96-99%,N=32… 98% (96-99…
#> 2 UCI E. coli 100% (93-100%,N=52) 99% (95-100%,N=1… 96% (92-99…
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
# WISCA antibiogram ----------------------------------------------------
@@ -774,7 +774,7 @@ antibiogram(example_isolates,
syndromic_group = "ward",
wisca = TRUE
)
#> # An Antibiogram: 3 × 4
#> # An antibiogram: 3 × 4
#> # Type: WISCA with 95% CI
#> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹
#> <chr> <chr> <chr>
@@ -784,7 +784,7 @@ antibiogram(example_isolates,
#> # ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`
#> # ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` <chr>
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
#> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram
#> # or use it directly in R Markdown or Quarto, see ?antibiogram
# Print the output for R Markdown / Quarto -----------------------------