Join microorganisms to a Data Set

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"))
#> ℹ Function `as.mo()` is uncertain about "K. pneumoniae" (assuming
#>   Klebsiella pneumoniae). Run `mo_uncertainties()` to review this.
#>             mo              fullname  kingdom         phylum
#> 1 B_KLBSL_PNMN Klebsiella pneumoniae Bacteria Proteobacteria
#>                 class            order             family      genus    species
#> 1 Gammaproteobacteria Enterobacterales Enterobacteriaceae Klebsiella pneumoniae
#>   subspecies    rank            ref species_id source prevalence
#> 1            species Trevisan, 1887     777151   LPSN          1
#>                                                                          snomed
#> 1 1098101000112102, 446870005, 1098201000112108, 409801009, 56415008, 714315002
left_join_microorganisms("B_KLBSL_PNMN")
#>             mo              fullname  kingdom         phylum
#> 1 B_KLBSL_PNMN Klebsiella pneumoniae Bacteria Proteobacteria
#>                 class            order             family      genus    species
#> 1 Gammaproteobacteria Enterobacterales Enterobacteriaceae Klebsiella pneumoniae
#>   subspecies    rank            ref species_id source prevalence
#> 1            species Trevisan, 1887     777151   LPSN          1
#>                                                                          snomed
#> 1 1098101000112102, 446870005, 1098201000112108, 409801009, 56415008, 714315002

# \donttest{
if (require("dplyr")) {
  example_isolates %>%
    left_join_microorganisms() %>% 
    colnames()
 
  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)
  df_joined <- left_join_microorganisms(df, "bacteria")
  colnames(df_joined)
}
#> Joining, by = "mo"
#> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia
#>   coli) and "S. aureus" (assuming Staphylococcus aureus). Run
#>   `mo_uncertainties()` to review these uncertainties.
#>  [1] "date"       "bacteria"   "fullname"   "kingdom"    "phylum"    
#>  [6] "class"      "order"      "family"     "genus"      "species"   
#> [11] "subspecies" "rank"       "ref"        "species_id" "source"    
#> [16] "prevalence" "snomed"    
# }