Join microorganisms to a Data Set

Source: R/join_microorganisms.R

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

Stable Lifecycle


The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.

If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.

Read more on Our Website!

On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!

Examples

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

# \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)
}
# }