# Join a table with <code>microorganisms</code> — join • AMR (for R)
Join the dataset microorganisms easily to an existing table or character vector.

# Join a table with `microorganisms`

`join.Rd`

Join the dataset `microorganisms` easily to an existing table or character vector.

    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 table to join, or character vector
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` (like `by = "bacteria_id"`), or another column in `microorganisms` (but then it should be named, like `by = c("my_genus_species" = "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.
... | other parameters to pass on to `dplyr::join`.

## Details

Note: As opposed to the `join` functions of `dplyr`, characters vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix. See `join` for more information.

## Examples

    # NOT RUN {
    left_join_microorganisms(as.mo("K. pneumoniae"))
    left_join_microorganisms("B_KLBSL_PNE")

    library(dplyr)
    septic_patients %>% left_join_microorganisms()

    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)
    # }