Join a table with microorganisms

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.

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

Examples

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

library(dplyr)
example_isolates %>% 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)