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# Join [microorganisms](https://amr-for-r.org/reference/microorganisms.md) to a Data Set
Join the data set
[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
easily to an existing data set or to a
[character](https://rdrr.io/r/base/character.html) vector.
## Usage
``` r
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](https://rdrr.io/r/base/character.html) vector. In case of
a [character](https://rdrr.io/r/base/character.html) vector, the
resulting [data.frame](https://rdrr.io/r/base/data.frame.html) 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`](https://amr-for-r.org/reference/as.mo.md) (created with
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md)) 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](https://amr-for-r.org/reference/microorganisms.md)
(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](https://rdrr.io/r/base/character.html) vector of length 2.
- ...:
Ignored, only in place to allow future extensions.
## Value
a [data.frame](https://rdrr.io/r/base/data.frame.html)
## Details
**Note:** As opposed to the `join()` functions of `dplyr`,
[character](https://rdrr.io/r/base/character.html) 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()`](https://rdatatable.gitlab.io/data.table/reference/merge.html)
and [`interaction()`](https://rdrr.io/r/base/interaction.html) functions
from base R will be used.
## Examples
``` r
left_join_microorganisms(as.mo("K. pneumoniae"))
#> # A tibble: 1 × 26
#> mo fullname status kingdom phylum class order family genus species
#> <mo> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…
#> # ℹ 16 more variables: subspecies <chr>, rank <chr>, ref <chr>,
#> # oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,
#> # lpsn_renamed_to <chr>, mycobank <chr>, mycobank_parent <chr>,
#> # mycobank_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,
#> # gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>
left_join_microorganisms("B_KLBSL_PNMN")
#> # A tibble: 1 × 26
#> mo fullname status kingdom phylum class order family genus species
#> <mo> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…
#> # ℹ 16 more variables: subspecies <chr>, rank <chr>, ref <chr>,
#> # oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>,
#> # lpsn_renamed_to <chr>, mycobank <chr>, mycobank_parent <chr>,
#> # mycobank_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,
#> # gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>
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)
#> [1] "date" "bacteria"
df_joined <- left_join_microorganisms(df, "bacteria")
colnames(df_joined)
#> [1] "date" "bacteria" "fullname"
#> [4] "status" "kingdom" "phylum"
#> [7] "class" "order" "family"
#> [10] "genus" "species" "subspecies"
#> [13] "rank" "ref" "oxygen_tolerance"
#> [16] "source" "lpsn" "lpsn_parent"
#> [19] "lpsn_renamed_to" "mycobank" "mycobank_parent"
#> [22] "mycobank_renamed_to" "gbif" "gbif_parent"
#> [25] "gbif_renamed_to" "prevalence" "snomed"
# \donttest{
if (require("dplyr")) {
example_isolates %>%
left_join_microorganisms() %>%
colnames()
}
#> Joining, by = "mo"
#> [1] "date" "patient" "age"
#> [4] "gender" "ward" "mo"
#> [7] "PEN" "OXA" "FLC"
#> [10] "AMX" "AMC" "AMP"
#> [13] "TZP" "CZO" "FEP"
#> [16] "CXM" "FOX" "CTX"
#> [19] "CAZ" "CRO" "GEN"
#> [22] "TOB" "AMK" "KAN"
#> [25] "TMP" "SXT" "NIT"
#> [28] "FOS" "LNZ" "CIP"
#> [31] "MFX" "VAN" "TEC"
#> [34] "TCY" "TGC" "DOX"
#> [37] "ERY" "CLI" "AZM"
#> [40] "IPM" "MEM" "MTR"
#> [43] "CHL" "COL" "MUP"
#> [46] "RIF" "fullname" "status"
#> [49] "kingdom" "phylum" "class"
#> [52] "order" "family" "genus"
#> [55] "species" "subspecies" "rank"
#> [58] "ref" "oxygen_tolerance" "source"
#> [61] "lpsn" "lpsn_parent" "lpsn_renamed_to"
#> [64] "mycobank" "mycobank_parent" "mycobank_renamed_to"
#> [67] "gbif" "gbif_parent" "gbif_renamed_to"
#> [70] "prevalence" "snomed"
# }
```