Add column to table in model description with code for each parameter #54

Author: mcsiple

inst/Documentation/ProjectionModel.Rmd

@@ -103,16 +103,37 @@ Description=c(#User-specified parameters
               "Number of animals of age $a$ at the start of year $y$",
               "Number of animals aged 1 and older at the start of year $y$",
               "Mortality due to bycatch of animals of age $a$ in year $y$")
+Code <- c(#User-specified parameters
+         "S0",
+         "S1plus",
+         "nages",
+         "lambdaMax",
+         "AgeMat + 1",
+         "ConstantF",
+         # Parameters derived from user-specified parameters
+         "Fec0",
+         "fmax",
+         "K1plus",
+         "z",
+         # Derived variables
+         "--", # need double dash for using in kableExtra
+         "--",
+         "--",
+         "--")
 
 Symbol_definitions <- data.frame(cbind(Symbol,
-                                      Description))
+                                      Description, Code))
+Symbol_definitions$Code <- cell_spec(Symbol_definitions$Code, font_size = 12, extra_css = "font-family:'Monaco', sans-serif;")
+  
 knitr::kable(format="html", #html  - change to pandoc for ms word 
              Symbol_definitions, 
              escape = FALSE) %>% 
             kable_styling('bordered') %>%
             pack_rows('User-specified parameters', 1, 6, label_row_css = "font-style: italic;border-bottom: 1px solid black;") %>%
-            pack_rows('Parameters derived from user-specified parameters', 7, 10, label_row_css = "font-style: italic;border-bottom: 1px solid black;") %>%
-            pack_rows('Derived variables', 11, 14, label_row_css = "font-style: italic;border-bottom: 1px solid black;")
+            pack_rows('Parameters derived from user-specified parameters', 7, 10, 
+                      label_row_css = "font-style: italic;border-bottom: 1px solid black;") %>%
+            pack_rows('Derived variables', 11, 14, 
+                      label_row_css = "font-style: italic;border-bottom: 1px solid black;")
 ```
 
 ### Performance measures

inst/Documentation/ProjectionModel.html

@@ -61,11 +61,14 @@ <h3>Population model</h3>
 <th style="text-align:left;">
 Description
 </th>
+<th style="text-align:left;">
+Code
+</th>
 </tr>
 </thead>
 <tbody>
 <tr grouplength="6">
-<td colspan="2" style="font-style: italic;border-bottom: 1px solid black;">
+<td colspan="3" style="font-style: italic;border-bottom: 1px solid black;">
 <strong>User-specified parameters</strong>
 </td>
 </tr>
@@ -76,6 +79,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Pup or calf survival
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">S0</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -84,6 +90,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Survival of individuals aged 1+
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">S1plus</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -92,6 +101,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Plus-group age
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">nages</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -100,6 +112,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Maximum steady rate of increase (population growth rate)
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">lambdaMax</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -108,6 +123,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Age at first parturition
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">AgeMat + 1</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -116,9 +134,12 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Bycatch mortality rate in year <span class="math inline">\(y\)</span> (specified by the user or computed from the user-specified total bycatch mortality)
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">ConstantF</span>
+</td>
 </tr>
 <tr grouplength="4">
-<td colspan="2" style="font-style: italic;border-bottom: 1px solid black;">
+<td colspan="3" style="font-style: italic;border-bottom: 1px solid black;">
 <strong>Parameters derived from user-specified parameters</strong>
 </td>
 </tr>
@@ -129,6 +150,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Fecundity (pregnancy rate) at pre-exploitation equilibrium
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">Fec0</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -137,6 +161,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Maximum theoretical fecundity (pregnancy rate)
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">fmax</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -145,6 +172,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Carrying capacity in terms of 1+ component of the population
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">K1plus</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -153,9 +183,12 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Degree of compensation
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">z</span>
+</td>
 </tr>
 <tr grouplength="4">
-<td colspan="2" style="font-style: italic;border-bottom: 1px solid black;">
+<td colspan="3" style="font-style: italic;border-bottom: 1px solid black;">
 <strong>Derived variables</strong>
 </td>
 </tr>
@@ -166,6 +199,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Number of mature animals of age <span class="math inline">\(a\)</span> at the start of year <span class="math inline">\(y\)</span>
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">–</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -174,6 +210,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Number of animals of age <span class="math inline">\(a\)</span> at the start of year <span class="math inline">\(y\)</span>
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">–</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -182,6 +221,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Number of animals aged 1 and older at the start of year <span class="math inline">\(y\)</span>
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">–</span>
+</td>
 </tr>
 <tr>
 <td style="text-align:left;padding-left: 2em;" indentlevel="1">
@@ -190,6 +232,9 @@ <h3>Population model</h3>
 <td style="text-align:left;">
 Mortality due to bycatch of animals of age <span class="math inline">\(a\)</span> in year <span class="math inline">\(y\)</span>
 </td>
+<td style="text-align:left;">
+<span style="     font-family:&#39;Monaco&#39;, sans-serif;font-size: 12px;">–</span>
+</td>
 </tr>
 </tbody>
 </table>
@@ -590,4 +635,4 @@ <h4>Compensation</h4>
   })();
 </script>
 
-</body>
+</body>