rlang dependency, new fungi

man/mo_source.Rd

@@ -15,6 +15,8 @@ get_mo_source()
 }
 \description{
 These functions can be used to predefine your own reference to be used in \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}.
+
+This is \strong{the fastest way} to have your organisation (or analysis) specific codes picked up and translated by this package.
 }
 \details{
 The reference file can be a text file seperated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
@@ -25,38 +27,66 @@ The reference file can be a text file seperated with commas (CSV) or tabs or pip
 
 Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file used by this package will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
 }
+\section{How it works}{
+
+Imagine this data on a sheet of an Excel file (mo codes were looked up in the `microorganisms` data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
+\preformatted{
+  |         A          |      B      |
+--|--------------------|-------------|
+1 | Organisation XYZ   | mo          |
+2 | lab_mo_ecoli       | B_ESCHR_COL |
+3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
+4 |                    |             |
+}
+
+We save it as \code{'home/me/ourcodes.xlsx'}. Now we have to set it as a source:
+\preformatted{
+set_mo_source("home/me/ourcodes.xlsx")
+# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
+}
+
+It has now created a file "~/.mo_source.rds" with the contents of our Excel file. It it an R specific format with great compression.
+
+And now we can use it in our functions:
+\preformatted{
+as.mo("lab_mo_ecoli")
+# B_ESCHR_COL
+
+mo_genus("lab_mo_kpneumoniae")
+# "Klebsiella"
+}
+
+If we edit the Excel file to, let's say, this:
+\preformatted{
+  |         A          |      B      |
+--|--------------------|-------------|
+1 | Organisation XYZ   | mo          |
+2 | lab_mo_ecoli       | B_ESCHR_COL |
+3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
+4 | lab_Staph_aureus   | B_STPHY_AUR |
+5 |                    |             |
+}
+
+...any new usage of an MO function in this package will update your data:
+\preformatted{
+as.mo("lab_mo_ecoli")
+# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
+# B_ESCHR_COL
+
+mo_genus("lab_Staph_aureus")
+# "Staphylococcus"
+}
+
+To remove the reference completely, just use any of these:
+\preformatted{
+set_mo_source("")
+set_mo_source(NULL)
+# Removed mo_source file '~/.mo_source.rds'.
+}
+}
+
 \section{Read more on our website!}{
 
 On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
 }
 
-\examples{
-\dontrun{
-
-# 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("home/me/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"
-}
-}