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mo_source improvement

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dr. M.S. (Matthijs) Berends
2019-03-01 09:34:04 +01:00
parent 2565b60024
commit c5efb272fd
21 changed files with 324 additions and 294 deletions
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13
docs/reference/mo_source.html
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@ -278,12 +278,15 @@ This is the fastest way to have your organisation (or analysis) specific codes p
set_mo_source("home/me/ourcodes.xlsx")
# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
</pre>
<p>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.</p>
<p>It has now created a file "~/.mo_source.rds" with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.</p>
<p>And now we can use it in our functions:</p><pre>
as.mo("lab_mo_ecoli")
# B_ESCHR_COL
[1] B_ESCHR_COL
mo_genus("lab_mo_kpneumoniae")
# "Klebsiella"
[1] "Klebsiella"
# other input values still work too
as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
[1] B_ESCHR_COL B_ESCHR_COL B_ESCHR_COL
</pre>
<p>If we edit the Excel file to, let's say, this:</p><pre>
| A | B |
@ -297,9 +300,9 @@ as.mo("lab_mo_ecoli")
<p>...any new usage of an MO function in this package will update your data:</p><pre>
as.mo("lab_mo_ecoli")
# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
# B_ESCHR_COL
[1] B_ESCHR_COL
mo_genus("lab_Staph_aureus")
# "Staphylococcus"
[1] "Staphylococcus"
</pre>
<p>To remove the reference completely, just use any of these:</p><pre>
set_mo_source("")