Use predefined reference data set

These functions can be used to predefine your own reference to be used in as.mo and consequently all mo_* functions like mo_genus and mo_gramstain.

set_mo_source(path)

get_mo_source()

Arguments

path	location of your reference file, see Details

Details

The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the readxl package installed.

set_mo_source will check the file for validity: it must be a data.frame, must have a column named "mo" which contains values from microorganisms$mo and must have a reference column with your own defined values. If all tests pass, set_mo_source will read the file into R and export it to "~/.mo_source.rds". This compressed data file will then be used at default for MO determination (function as.mo and consequently all mo_* functions like mo_genus and mo_gramstain). The location of the original file will be saved as option with options(mo_source = path). Its timestamp will be saved with options(mo_source_datetime = ...).

get_mo_source will return the data set by reading "~/.mo_source.rds" with readRDS. If the original file has changed (the file defined with path), it will call set_mo_source to update the data file automatically.

Reading an Excel file (.xlsx) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by get_mo_source in only a couple of microseconds (a millionth of a second).

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive 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

# NOT RUN {
# imagine this Excel file (mo codes looked up in `microorganisms` data set):
#            A                B
# 1  our code            mo
# 2  lab_mo_ecoli        B_ESCHR_COL
# 3  lab_mo_kpneumoniae  B_KLBSL_PNE

# 1. We save it as 'home/me/ourcodes.xlsx'

# 2. We use it for input:
set_mo_source("C:\path\ourcodes.xlsx")
#> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.

# 3. And use it in our functions:
as.mo("lab_mo_ecoli")
#> B_ESCHR_COL

mo_genus("lab_mo_kpneumoniae")
#> "Klebsiella"

# 4. It will look for changes itself:
# (add new row to the Excel file and save it)

mo_genus("lab_mo_kpneumoniae")
#> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#> "Klebsiella"
# }