join {AMR}

Join microorganisms to a Data Set

Description

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

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.

Value

a data.frame

Examples

left_join_microorganisms(as.mo("K. pneumoniae"))
left_join_microorganisms("B_KLBSL_PNMN")

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)


if (require("dplyr")) {
  example_isolates %>%
    left_join_microorganisms() %>%
    colnames()
}