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diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html
index bbfb592..0216e4e 100644
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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span>
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<h1>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</h1>
@@ -115,210 +46,78 @@ The text file is not included in the package as its licence is not clear.</p>
</div>
-
- <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
+ <div id="format">
+ <h2>Format</h2>
<p>A list containing the scenario names in a character vector called 'names',
the drift percentiles in a matrix called 'drift', interception percentages in
a matrix called 'interception' and the runoff/drainage percentages for Step 2
calculations in a matrix called 'rd'.</p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
-<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
- <span class='co'># This is the code that was used to extract the data</span>
- <span class='no'>scenario_path</span> <span class='kw'>&lt;-</span> <span class='st'>"inst/extdata/FOCUS_Step_12_scenarios.txt"</span>
- <span class='no'>scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/readLines.html'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>9</span>:<span class='fl'>38</span>]
- <span class='no'>FOCUS_Step_12_scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>()
- <span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>scenarios</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
- <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span> <span class='kw'>=</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
- <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>sce</span>) <span class='kw'>&lt;-</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
- <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>drift</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>3</span>:<span class='fl'>11</span>]
- <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>interception</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>12</span>:<span class='fl'>15</span>]
- <span class='no'>sce_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/readLines.html'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>41</span>:<span class='fl'>46</span>]
- <span class='no'>rd</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>sce_2</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>)[<span class='fl'>1</span>:<span class='fl'>2</span>]
- <span class='no'>rd_mat</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='no'>rd</span>$<span class='no'>V2</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
- <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>rd_mat</span>) <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Oct-Feb"</span>, <span class='st'>"Mar-May"</span>, <span class='st'>"Jun-Sep"</span>),
- <span class='kw'>Region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"South"</span>))
- <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>rd</span> <span class='kw'>=</span> <span class='no'>rd_mat</span>
- <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>FOCUS_Step_12_scenarios</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/FOCUS_Step_12_scenarios.RData"</span>)
-}
-
-<span class='co'># And this is the resulting data</span>
-<span class='no'>FOCUS_Step_12_scenarios</span></div><div class='output co'>#&gt; $names
-#&gt; [1] "cereals, spring" "cereals, winter"
-#&gt; [3] "citrus" "cotton"
-#&gt; [5] "field beans" "grass / alfalfa"
-#&gt; [7] "hops" "legumes"
-#&gt; [9] "maize" "oil seed rape, spring"
-#&gt; [11] "oil seed rape, winter" "olives"
-#&gt; [13] "pome / stone fruit, early applns" "pome / stone fruit, late applns"
-#&gt; [15] "potatoes" "soybeans"
-#&gt; [17] "sugar beets" "sunflowers"
-#&gt; [19] "tobacco" "vegetables, bulb"
-#&gt; [21] "vegetables, fruiting" "vegetables, leafy"
-#&gt; [23] "vegetables, root" "vines, early applns"
-#&gt; [25] "vines, late applns" "appln, aerial"
-#&gt; [27] "appln, hand (crop &lt; 50 cm)" "appln, hand (crop &gt; 50 cm)"
-#&gt; [29] "no drift (incorp or seed trtmt)"
-#&gt;
-#&gt; $drift
-#&gt; 1 2 3 4 5 6
-#&gt; cereals, spring 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; cereals, winter 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; citrus 15.725 12.129 11.011 10.124 9.743 9.204
-#&gt; cotton 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; field beans 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; grass / alfalfa 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; hops 19.326 17.723 15.928 15.378 15.114 14.902
-#&gt; legumes 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; maize 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; oil seed rape, spring 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; oil seed rape, winter 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; olives 15.725 12.129 11.011 10.124 9.743 9.204
-#&gt; pome / stone fruit, early applns 29.197 25.531 23.960 23.603 23.116 22.760
-#&gt; pome / stone fruit, late applns 15.725 12.129 11.011 10.124 9.743 9.204
-#&gt; potatoes 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; soybeans 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; sugar beets 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; sunflowers 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; tobacco 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; vegetables, bulb 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; vegetables, fruiting 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; vegetables, leafy 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; vegetables, root 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; vines, early applns 2.699 2.496 2.546 2.499 2.398 2.336
-#&gt; vines, late applns 8.028 7.119 6.898 6.631 6.636 6.431
-#&gt; appln, aerial 33.200 33.200 33.200 33.200 33.200 33.200
-#&gt; appln, hand (crop &lt; 50 cm) 2.759 2.438 2.024 1.862 1.794 1.631
-#&gt; appln, hand (crop &gt; 50 cm) 8.028 7.119 6.898 6.631 6.636 6.431
-#&gt; no drift (incorp or seed trtmt) 0.000 0.000 0.000 0.000 0.000 0.000
-#&gt; 7 8 &gt;8
-#&gt; cereals, spring 1.578 1.512 1.512
-#&gt; cereals, winter 1.578 1.512 1.512
-#&gt; citrus 9.102 8.656 8.656
-#&gt; cotton 1.578 1.512 1.512
-#&gt; field beans 1.578 1.512 1.512
-#&gt; grass / alfalfa 1.578 1.512 1.512
-#&gt; hops 14.628 13.520 13.520
-#&gt; legumes 1.578 1.512 1.512
-#&gt; maize 1.578 1.512 1.512
-#&gt; oil seed rape, spring 1.578 1.512 1.512
-#&gt; oil seed rape, winter 1.578 1.512 1.512
-#&gt; olives 9.102 8.656 8.656
-#&gt; pome / stone fruit, early applns 22.690 22.241 22.241
-#&gt; pome / stone fruit, late applns 9.102 8.656 8.656
-#&gt; potatoes 1.578 1.512 1.512
-#&gt; soybeans 1.578 1.512 1.512
-#&gt; sugar beets 1.578 1.512 1.512
-#&gt; sunflowers 1.578 1.512 1.512
-#&gt; tobacco 1.578 1.512 1.512
-#&gt; vegetables, bulb 1.578 1.512 1.512
-#&gt; vegetables, fruiting 1.578 1.512 1.512
-#&gt; vegetables, leafy 1.578 1.512 1.512
-#&gt; vegetables, root 1.578 1.512 1.512
-#&gt; vines, early applns 2.283 2.265 2.265
-#&gt; vines, late applns 6.227 6.173 6.173
-#&gt; appln, aerial 33.200 33.200 33.200
-#&gt; appln, hand (crop &lt; 50 cm) 1.578 1.512 1.512
-#&gt; appln, hand (crop &gt; 50 cm) 6.227 6.173 6.173
-#&gt; no drift (incorp or seed trtmt) 0.000 0.000 0.000
-#&gt;
-#&gt; $interception
-#&gt; no interception minimal crop cover
-#&gt; cereals, spring 0 0.00
-#&gt; cereals, winter 0 0.00
-#&gt; citrus 0 0.80
-#&gt; cotton 0 0.30
-#&gt; field beans 0 0.25
-#&gt; grass / alfalfa 0 0.40
-#&gt; hops 0 0.20
-#&gt; legumes 0 0.25
-#&gt; maize 0 0.25
-#&gt; oil seed rape, spring 0 0.40
-#&gt; oil seed rape, winter 0 0.40
-#&gt; olives 0 0.70
-#&gt; pome / stone fruit, early applns 0 0.20
-#&gt; pome / stone fruit, late applns 0 0.20
-#&gt; potatoes 0 0.15
-#&gt; soybeans 0 0.20
-#&gt; sugar beets 0 0.20
-#&gt; sunflowers 0 0.20
-#&gt; tobacco 0 0.20
-#&gt; vegetables, bulb 0 0.10
-#&gt; vegetables, fruiting 0 0.25
-#&gt; vegetables, leafy 0 0.25
-#&gt; vegetables, root 0 0.25
-#&gt; vines, early applns 0 0.40
-#&gt; vines, late applns 0 0.40
-#&gt; appln, aerial 0 0.20
-#&gt; appln, hand (crop &lt; 50 cm) 0 0.20
-#&gt; appln, hand (crop &gt; 50 cm) 0 0.20
-#&gt; no drift (incorp or seed trtmt) 0 0.00
-#&gt; average crop cover full canopy
-#&gt; cereals, spring 0.20 0.70
-#&gt; cereals, winter 0.20 0.70
-#&gt; citrus 0.80 0.80
-#&gt; cotton 0.60 0.75
-#&gt; field beans 0.40 0.70
-#&gt; grass / alfalfa 0.60 0.75
-#&gt; hops 0.50 0.70
-#&gt; legumes 0.50 0.70
-#&gt; maize 0.50 0.75
-#&gt; oil seed rape, spring 0.70 0.75
-#&gt; oil seed rape, winter 0.70 0.75
-#&gt; olives 0.70 0.70
-#&gt; pome / stone fruit, early applns 0.40 0.65
-#&gt; pome / stone fruit, late applns 0.40 0.65
-#&gt; potatoes 0.50 0.70
-#&gt; soybeans 0.50 0.75
-#&gt; sugar beets 0.70 0.75
-#&gt; sunflowers 0.50 0.75
-#&gt; tobacco 0.70 0.75
-#&gt; vegetables, bulb 0.25 0.40
-#&gt; vegetables, fruiting 0.50 0.70
-#&gt; vegetables, leafy 0.40 0.70
-#&gt; vegetables, root 0.50 0.70
-#&gt; vines, early applns 0.50 0.60
-#&gt; vines, late applns 0.50 0.60
-#&gt; appln, aerial 0.50 0.70
-#&gt; appln, hand (crop &lt; 50 cm) 0.50 0.70
-#&gt; appln, hand (crop &gt; 50 cm) 0.50 0.70
-#&gt; no drift (incorp or seed trtmt) 0.00 0.00
-#&gt;
-#&gt; $rd
-#&gt; Region
-#&gt; Time North South
-#&gt; Oct-Feb 5 4
-#&gt; Mar-May 2 4
-#&gt; Jun-Sep 2 3
-#&gt; </div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span> <span class="co"># This is the code that was used to extract the data</span></span></span>
+<span class="r-in"><span> <span class="va">scenario_path</span> <span class="op">&lt;-</span> <span class="st">"inst/extdata/FOCUS_Step_12_scenarios.txt"</span></span></span>
+<span class="r-in"><span> <span class="va">scenarios</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">9</span><span class="op">:</span><span class="fl">38</span><span class="op">]</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span>
+<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">sce</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">scenarios</span>, sep <span class="op">=</span> <span class="st">"\t"</span>, header <span class="op">=</span> <span class="cn">TRUE</span>, check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
+<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'scenarios' not found</span>
+<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span> <span class="op">=</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span>
+<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">drift</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">11</span><span class="op">]</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span>
+<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">interception</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">12</span><span class="op">:</span><span class="fl">15</span><span class="op">]</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span>
+<span class="r-in"><span> <span class="va">sce_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">41</span><span class="op">:</span><span class="fl">46</span><span class="op">]</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span>
+<span class="r-in"><span> <span class="va">rd</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">sce_2</span>, sep <span class="op">=</span> <span class="st">"\t"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce_2' not found</span>
+<span class="r-in"><span> <span class="va">rd_mat</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="va">rd</span><span class="op">$</span><span class="va">V2</span>, nrow <span class="op">=</span> <span class="fl">3</span>, byrow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd' not found</span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">rd_mat</span><span class="op">)</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>Time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Oct-Feb"</span>, <span class="st">"Mar-May"</span>, <span class="st">"Jun-Sep"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> Region <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"North"</span>, <span class="st">"South"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> object 'rd_mat' not found</span>
+<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">rd</span> <span class="op">=</span> <span class="va">rd_mat</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd_mat' not found</span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">FOCUS_Step_12_scenarios</span>, file <span class="op">=</span> <span class="st">"data/FOCUS_Step_12_scenarios.RData"</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory'</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in gzfile(file, "wb"):</span> cannot open the connection</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># And this is the resulting data</span></span></span>
+<span class="r-in"><span><span class="va">FOCUS_Step_12_scenarios</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> list()</span>
+</code></pre></div>
+ </div>
</div>
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