P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 22:01:49 +02:00
Code Releases Activity

(v0.9.0) website fixes

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-11-30 12:01:50 +01:00
parent c9aefd1841
commit 56ce9bf665
21 changed files with 300 additions and 302 deletions
Download Patch File Download Diff File Expand all files Collapse all files

21
docs/reference/mo_source.html
View File

@ -260,12 +260,12 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>Reading an Excel file (<code>.xlsx</code>) 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()</code> in only a couple of microseconds (a millionth of a second).</p><h3>How it works</h3>
<p>Imagine this data on a sheet of an Excel file (mo codes were looked up in the <code>microorganisms</code> data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:</p><pre> | A | B |
--|--------------------|-------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COL |
3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
4 | | |
<p>Imagine this data on a sheet of an Excel file (mo codes were looked up in the <code>microorganisms</code> data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:</p><pre> | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
4 | | |
</pre>
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p><pre>set_mo_source("home/me/ourcodes.xlsx")
@ -274,7 +274,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>It has now created a file <code>"~/.mo_source.rds"</code> 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")
\[1\] B_ESCHR_COLI
[1] B_ESCHR_COLI
mo_genus("lab_mo_kpneumoniae")
[1] "Klebsiella"
@ -284,7 +284,7 @@ as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
[1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
</pre>
<p>If we edit the Excel file to, let's say, this:</p><pre> | A | B |
<p>If we edit the Excel file to, let's say, by adding row 4 like this:</p><pre> | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
@ -293,7 +293,7 @@ as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
5 | | |
</pre>
<p>...any new usage of an MO function in this package will update your data:</p><pre>as.mo("lab_mo_ecoli")
<p>...any new usage of an MO function in this package will update your data file:</p><pre>as.mo("lab_mo_ecoli")
# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
[1] B_ESCHR_COLI
@ -301,8 +301,7 @@ mo_genus("lab_Staph_aureus")
[1] "Staphylococcus"
</pre>
<p>To remove the reference completely, just use any of these:</p><pre>set_mo_source("")
set_mo_source(NULL)
<p>To remove the reference data file completely, just use <code>""</code> or <code>NULL</code> as input for <code>[set_mo_source()]</code>:</p><pre>set_mo_source(NULL)
# Removed mo_source file '~/.mo_source.rds'.
</pre>