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age_groups fix

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dr. M.S. (Matthijs) Berends
2019-02-27 11:36:12 +01:00
parent 4ba2ff68e0
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41 changed files with 450 additions and 386 deletions
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docs/reference/mo_source.html
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>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 <code>readxl</code> package installed.</p>
<p>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</code> package installed.</p>
<p><code>set_mo_source</code> will check the file for validity: it must be a <code>data.frame</code>, must have a column named <code>"mo"</code> which contains values from <code>microorganisms$mo</code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source</code> will read the file into R and export it to <code>"~/.mo_source.rds"</code>. This compressed data file will then be used at default for MO determination (function <code><a href='as.mo.html'>as.mo</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus</a></code> and <code><a href='mo_property.html'>mo_gramstain</a></code>). The location of the original file will be saved as option with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options</a>(mo_source = path)</code>. Its timestamp will be saved with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options</a>(mo_source_datetime = ...)</code>.</p>
<p><code>get_mo_source</code> will return the data set by reading <code>"~/.mo_source.rds"</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/readRDS'>readRDS</a></code>. If the original file has changed (the file defined with <code>path</code>), it will call <code>set_mo_source</code> to update the data file automatically.</p>
<p>Reading an Excel file (<code>.xlsx</code>) 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 <code>get_mo_source</code> in only a couple of microseconds (a millionth of a second).</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>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="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
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># imagine this Excel file (mo codes looked up in `microorganisms` data set):</span>
<span class='co'># A B</span>
<span class='co'># 1 our code mo</span>
<span class='co'># 2 lab_mo_ecoli B_ESCHR_COL</span>
<span class='co'># 3 lab_mo_kpneumoniae B_KLBSL_PNE</span>
# 1. We save it as 'home/me/ourcodes.xlsx'
<span class='co'># 1. We save it as 'home/me/ourcodes.xlsx'</span>
# 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'.
<span class='co'># 2. We use it for input:</span>
<span class='fu'>set_mo_source</span>(<span class='st'>"home/me/ourcodes.xlsx"</span>)
<span class='co'>#&gt; Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.</span>
# 3. And use it in our functions:
as.mo("lab_mo_ecoli")
#> B_ESCHR_COL
<span class='co'># 3. And use it in our functions:</span>
<span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"lab_mo_ecoli"</span>)
<span class='co'>#&gt; B_ESCHR_COL</span>
mo_genus("lab_mo_kpneumoniae")
#> "Klebsiella"
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_mo_kpneumoniae"</span>)
<span class='co'>#&gt; "Klebsiella"</span>
# 4. It will look for changes itself:
# (add new row to the Excel file and save it)
<span class='co'># 4. It will look for changes itself:</span>
<span class='co'># (add new row to the Excel file and save it)</span>
mo_genus("lab_mo_kpneumoniae")
#> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#> "Klebsiella"
# }
</pre>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"lab_mo_kpneumoniae"</span>)
<span class='co'>#&gt; Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.</span>
<span class='co'>#&gt; "Klebsiella"</span>
<span class='co'># }</span></pre>
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