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Join the data set microorganisms easily to an existing data set or to a character vector.

Usage

inner_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)

left_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)

right_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)

full_join_microorganisms(x, by = NULL, suffix = c("2", ""), ...)

semi_join_microorganisms(x, by = NULL, ...)

anti_join_microorganisms(x, by = NULL, ...)

Arguments

x

existing data set to join, or character vector. In case of a character vector, the resulting data.frame will contain a column 'x' with these values.

by

a variable to join by - if left empty will search for a column with class mo (created with as.mo()) or will be "mo" if that column name exists in x, could otherwise be a column name of x with values that exist in microorganisms$mo (such as by = "bacteria_id"), or another column in microorganisms (but then it should be named, like by = c("bacteria_id" = "fullname"))

suffix

if there are non-joined duplicate variables in x and y, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.

...

ignored, only in place to allow future extensions

Value

a data.frame

Details

Note: As opposed to the join() functions of dplyr, character vectors are supported and at default existing columns will get a suffix "2" and the newly joined columns will not get a suffix.

If the dplyr package is installed, their join functions will be used. Otherwise, the much slower merge() and interaction() functions from base R will be used.

Examples

left_join_microorganisms(as.mo("K. pneumoniae"))
#> # A tibble: 1 × 23
#>   mo           fullname   status kingdom phylum class order family genus species
#>   <mo>         <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>  
#> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…
#> # ℹ 13 more variables: subspecies <chr>, rank <chr>, ref <chr>,
#> #   oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,
#> #   lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,
#> #   gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>
left_join_microorganisms("B_KLBSL_PNMN")
#> # A tibble: 1 × 23
#>   mo           fullname   status kingdom phylum class order family genus species
#>   <mo>         <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>  
#> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…
#> # ℹ 13 more variables: subspecies <chr>, rank <chr>, ref <chr>,
#> #   oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,
#> #   lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,
#> #   gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>

df <- data.frame(
  date = seq(
    from = as.Date("2018-01-01"),
    to = as.Date("2018-01-07"),
    by = 1
  ),
  bacteria = as.mo(c(
    "S. aureus", "MRSA", "MSSA", "STAAUR",
    "E. coli", "E. coli", "E. coli"
  )),
  stringsAsFactors = FALSE
)
colnames(df)
#> [1] "date"     "bacteria"

df_joined <- left_join_microorganisms(df, "bacteria")
colnames(df_joined)
#>  [1] "date"             "bacteria"         "fullname"         "status"          
#>  [5] "kingdom"          "phylum"           "class"            "order"           
#>  [9] "family"           "genus"            "species"          "subspecies"      
#> [13] "rank"             "ref"              "oxygen_tolerance" "source"          
#> [17] "lpsn"             "lpsn_parent"      "lpsn_renamed_to"  "gbif"            
#> [21] "gbif_parent"      "gbif_renamed_to"  "prevalence"       "snomed"          

# \donttest{
if (require("dplyr")) {
  example_isolates %>%
    left_join_microorganisms() %>%
    colnames()
}
#> Joining, by = "mo"
#>  [1] "date"             "patient"          "age"              "gender"          
#>  [5] "ward"             "mo"               "PEN"              "OXA"             
#>  [9] "FLC"              "AMX"              "AMC"              "AMP"             
#> [13] "TZP"              "CZO"              "FEP"              "CXM"             
#> [17] "FOX"              "CTX"              "CAZ"              "CRO"             
#> [21] "GEN"              "TOB"              "AMK"              "KAN"             
#> [25] "TMP"              "SXT"              "NIT"              "FOS"             
#> [29] "LNZ"              "CIP"              "MFX"              "VAN"             
#> [33] "TEC"              "TCY"              "TGC"              "DOX"             
#> [37] "ERY"              "CLI"              "AZM"              "IPM"             
#> [41] "MEM"              "MTR"              "CHL"              "COL"             
#> [45] "MUP"              "RIF"              "fullname"         "status"          
#> [49] "kingdom"          "phylum"           "class"            "order"           
#> [53] "family"           "genus"            "species"          "subspecies"      
#> [57] "rank"             "ref"              "oxygen_tolerance" "source"          
#> [61] "lpsn"             "lpsn_parent"      "lpsn_renamed_to"  "gbif"            
#> [65] "gbif_parent"      "gbif_renamed_to"  "prevalence"       "snomed"          
# }