Enable markdown and rebuild docs

1 files changed, 14 insertions, 14 deletions

diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 78f6453..e758347 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -91,7 +91,7 @@ to be used with the FOCUS calculator.</p>
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
     <dl><dt>parent</dt>
 <dd><p>A list containing substance specific parameters, e.g.
-conveniently generated by [chent_focus_sw].</p></dd>
+conveniently generated by <a href="chent_focus_sw.html">chent_focus_sw</a>.</p></dd>
 
 
 <dt>rate</dt>
@@ -113,7 +113,7 @@ applications are given explicitly</p></dd>
 
 <dt>met</dt>
 <dd><p>A list containing metabolite specific parameters.  e.g.
-conveniently generated by [chent_focus_sw].  If not NULL,
+conveniently generated by <a href="chent_focus_sw.html">chent_focus_sw</a>.  If not NULL,
 the PEC is calculated for this compound, not the parent.</p></dd>
 
 
@@ -121,18 +121,18 @@ the PEC is calculated for this compound, not the parent.</p></dd>
 <dd><p>The fraction of the application rate reaching the waterbody
 via drift. If NA, this is derived from the scenario name and the number
 of applications via the drift data defined by the
-[FOCUS_Step_12_scenarios]</p></dd>
+<a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></p></dd>
 
 
 <dt>f_rd</dt>
 <dd><p>The fraction of the amount applied reaching the waterbody via
-runoff/drainage. At Step 1, it is assumed to be 10<!-- %, be it the -->
+runoff/drainage. At Step 1, it is assumed to be 10%, be it the
 parent or a metabolite</p></dd>
 
 
 <dt>scenario</dt>
 <dd><p>The name of the scenario. Must be one of the scenario
-names given in [FOCUS_Step_12_scenarios]</p></dd>
+names given in <a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></p></dd>
 
 
 <dt>region</dt>
@@ -174,21 +174,21 @@ should be written</p></dd>
     <div class="section level2">
     <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
     <p>The formulas for input to the waterbody via runoff/drainage of the
-  parent and subsequent formation of the metabolite in water is not
-  documented in the model description coming with the calculator. As one would
-  expect, this appears to be (as we get the same results) calculated by
-  multiplying the application rate with the molar weight
-  correction and the formation fraction in water/sediment systems.</p>
+parent and subsequent formation of the metabolite in water is not
+documented in the model description coming with the calculator. As one would
+expect, this appears to be (as we get the same results) calculated by
+multiplying the application rate with the molar weight
+correction and the formation fraction in water/sediment systems.</p>
 <p>Step 2 is not implemented.</p>
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
     <p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4).
- FOrum for the Co-ordination of pesticde fate models and their USe.
- http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic<!-- %20FOCUS_SWS_vc1.4.pdf --></p>
+FOrum for the Co-ordination of pesticde fate models and their USe.
+http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf</p>
 <p>Website of the Steps 1 and 2 calculator at the Joint Research
-  Center of the European Union:
-  http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p>
+Center of the European Union:
+http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p>
     </div>
 
     <div class="section level2">