diff --git a/404.html b/404.html index 37bc36c9..0976f49c 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 2.0.0.9026 + 2.0.0.9028 + + + + + +
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Data Set with 444 Microorganisms In Species Groups

+ Source: R/data.R +
microorganisms.groups.Rd
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A data set containing species groups and microbiological complexes, which are used in the clinical breakpoints table.

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Usage

+ 
microorganisms.groups
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Format

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A tibble with 444 observations and 4 variables:

  • mo_group
    ID of the species group / microbiological complex

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  • mo
    ID of the microorganism belonging in the species group / microbiological complex

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  • mo_group_name
    Name of the species group / microbiological complex, as retrieved with mo_name()

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  • mo_name
    Name of the microorganism belonging in the species group / microbiological complex, as retrieved with mo_name()

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Details

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Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

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See also

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as.mo() microorganisms

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Examples

+ 
microorganisms.groups
+#> # A tibble: 444 × 4
+#>    mo_group       mo           mo_group_name                   mo_name          
+#>    <mo>           <mo>         <chr>                           <chr>            
+#>  1 B_ACNTB_BMNN-C B_ACNTB_BMNN Acinetobacter baumannii complex Acinetobacter ba…
+#>  2 B_ACNTB_BMNN-C B_ACNTB_CLCC Acinetobacter baumannii complex Acinetobacter ca…
+#>  3 B_ACNTB_BMNN-C B_ACNTB_DJKS Acinetobacter baumannii complex Acinetobacter di…
+#>  4 B_ACNTB_BMNN-C B_ACNTB_NSCM Acinetobacter baumannii complex Acinetobacter no…
+#>  5 B_ACNTB_BMNN-C B_ACNTB_PITT Acinetobacter baumannii complex Acinetobacter pi…
+#>  6 B_ACNTB_BMNN-C B_ACNTB_SFRT Acinetobacter baumannii complex Acinetobacter se…
+#>  7 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex    Bacteroides frag…
+#>  8 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex    Bacteroides ovat…
+#>  9 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex    Bacteroides thet…
+#> 10 B_BCTRD_FRGL-C B_BCTRD_VLGT Bacteroides fragilis complex    Bacteroides vulg…
+#> # ℹ 434 more rows
+
+# these are all species in the Bacteroides fragilis group, as per WHONET:
+microorganisms.groups[microorganisms.groups$mo_group == "B_BCTRD_FRGL-C", ]
+#> # A tibble: 5 × 4
+#>   mo_group       mo           mo_group_name                mo_name              
+#>   <mo>           <mo>         <chr>                        <chr>                
+#> 1 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex Bacteroides fragilis 
+#> 2 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex Bacteroides ovatus   
+#> 3 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex Bacteroides thetaiot…
+#> 4 B_BCTRD_FRGL-C B_BCTRD_VLGT Bacteroides fragilis complex Bacteroides vulgatus 
+#> 5 B_BCTRD_FRGL-C B_PRBCT_DSTS Bacteroides fragilis complex Parabacteroides dist…
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+ + + + + + + diff --git a/reference/microorganisms.html b/reference/microorganisms.html index 2ee13478..43e3e25b 100644 --- a/reference/microorganisms.html +++ b/reference/microorganisms.html @@ -1,5 +1,5 @@ -Data Set with 52 158 Microorganisms — microorganisms • AMR (for R)Data Set with 52 169 Microorganisms — microorganisms • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9026 + 2.0.0.9028