Merge pull request #4 from WorldFishCenter/update-aes

update to publication style

R/xgb-model.R

@@ -149,9 +149,9 @@ run_xgmodel <- function(dataframe = NULL,
     tune::collect_predictions() %>%
     yardstick::roc_curve(cluster, feat_names, event_level = "second") %>%
     ggplot2::ggplot(ggplot2::aes(1 - specificity, sensitivity, color = .level)) +
-    ggplot2::theme_minimal() +
-    ggplot2::geom_line() +
-    ggplot2::geom_point(size = 0.5) +
+    ggpubr::theme_pubr() +
+    ggplot2::geom_line(size = 1) +
+    ggplot2::geom_point(size = 1) +
     ggplot2::geom_abline(slope = 1, intercept = 0, color = "grey", linetype = "dashed") +
     ggplot2::coord_cartesian(expand = FALSE) +
     ggplot2::scale_color_manual(values = timor.nutrients::palettes$clusters_palette) +

docs/afigures.html

@@ -142,14 +142,14 @@ <h1>
             <section class="normal" id="section-">
 <div id="afigures" class="section level1 hasAnchor" number="7">
 <h1><span class="header-section-number">7</span> Other figures<a href="afigures.html#afigures" class="anchor-section" aria-label="Anchor link to header"></a></h1>
-<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-13"></span>
-<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-13-1.png" alt="To define" width="864" />
+<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-14"></span>
+<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-14-1.png" alt="To define" width="864" />
 <p class="caption">
 Figure 7.1: To define
 </p>
 </div>
-<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-14"></span>
-<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-14-1.png" alt="To define" width="768" />
+<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-15"></span>
+<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-15-1.png" alt="To define" width="768" />
 <p class="caption">
 Figure 7.2: To define
 </p>

docs/distribution.html

@@ -145,26 +145,26 @@ <h1><span class="header-section-number">4</span> Nutrients distribution<a href="
 <p>This section presents the analyses that illustrates the distribution of nutrients within various components of small-scale fisheries in East Timor.</p>
 <div id="fish-groups" class="section level2 hasAnchor" number="4.1">
 <h2><span class="header-section-number">4.1</span> Fish groups<a href="distribution.html#fish-groups" class="anchor-section" aria-label="Anchor link to header"></a></h2>
-<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-2"></span>
-<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-2-1.png" alt="The bar chart illustrates the contribution of a variety of marine food sources to the Recommended Nutrient Intake (RNI) for six fundamental nutrients, based on a 100g portion. Each bar is a color-segmented stacked visual, with distinct hues corresponding to individual nutrients, and white numbers within indicating the specific percentage contribution of each nutrient. The chart incorporates the mean annual catch in metric tons for each marine species from 2018 to 2023, presented at the end of each bar, providing a view of both the nutritional value and the harvest volume of these essential food sources. The transparency of these values is adjusted to reflect each species' relative contribution to the mean annual catch" width="80%" />
+<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-3"></span>
+<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-3-1.png" alt="The bar chart illustrates the contribution of a variety of marine food sources to the Recommended Nutrient Intake (RNI) for six fundamental nutrients, based on a 100g portion. Each bar is a color-segmented stacked visual, with distinct hues corresponding to individual nutrients, and white numbers within indicating the specific percentage contribution of each nutrient. The chart incorporates the mean annual catch in metric tons for each marine species from 2018 to 2023, presented at the end of each bar, providing a view of both the nutritional value and the harvest volume of these essential food sources. The transparency of these values is adjusted to reflect each species' relative contribution to the mean annual catch" width="80%" />
 <p class="caption">
 Figure 4.1: The bar chart illustrates the contribution of a variety of marine food sources to the Recommended Nutrient Intake (RNI) for six fundamental nutrients, based on a 100g portion. Each bar is a color-segmented stacked visual, with distinct hues corresponding to individual nutrients, and white numbers within indicating the specific percentage contribution of each nutrient. The chart incorporates the mean annual catch in metric tons for each marine species from 2018 to 2023, presented at the end of each bar, providing a view of both the nutritional value and the harvest volume of these essential food sources. The transparency of these values is adjusted to reflect each species’ relative contribution to the mean annual catch
 </p>
 </div>
 </div>
 <div id="habitat-and-gear-type" class="section level2 hasAnchor" number="4.2">
 <h2><span class="header-section-number">4.2</span> Habitat and gear type<a href="distribution.html#habitat-and-gear-type" class="anchor-section" aria-label="Anchor link to header"></a></h2>
-<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-3"></span>
-<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-3-1.png" alt="Sankey diagram showing the relative distribution of key nutrients across various marine habitats and the corresponding extraction by different fishing gear types used in Timor-Est small-scale fisheries." width="672" />
+<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-4"></span>
+<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-4-1.png" alt="Sankey diagram showing the relative distribution of key nutrients across various marine habitats and the corresponding extraction by different fishing gear types used in Timor-Est small-scale fisheries." width="672" />
 <p class="caption">
 Figure 4.2: Sankey diagram showing the relative distribution of key nutrients across various marine habitats and the corresponding extraction by different fishing gear types used in Timor-Est small-scale fisheries.
 </p>
 </div>
 </div>
 <div id="nutritional-contribution-and-economic-profiling" class="section level2 hasAnchor" number="4.3">
 <h2><span class="header-section-number">4.3</span> Nutritional contribution and economic profiling<a href="distribution.html#nutritional-contribution-and-economic-profiling" class="anchor-section" aria-label="Anchor link to header"></a></h2>
-<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-4"></span>
-<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-4-1.png" alt="Nutritional and economic profiling of key fish groups within the Timor-Leste fishery.Panel A, Distribution of nutritional content among different functional fish groups: Small pelagics, Large pelagics, Small demersals, Large demersals, Sharks and rays and Other groups, that includes shrimps, molluscs, cephalopods and crustaceans. The plot shows the ranked contribution of each functional fish to the supply of calcium, omega-3, iron, protein, vitamin A, and zinc during the period 2018-2023. Panel B, Comparative analysis of nutritional score versus economic accessibility for key fish groups. This scatter plot displays the relationship between the cumulative nutritional score and the market price for various fish groups within Timor-Leste fishery. The x-axis quantifies the cumulative contribution to the Recommended Nutrient Intake (RNI) for six essential nutrients (zinc, protein, omega-3, calcium, iron, vitamin A) from a 100g portion of each fish group. The y-axis represents the average market price per kilogram for each group. Dot size and the accompanying numerical labels reflect the relative catch percentage of each group, serving as an index of accessibility and availability. Panel C, The bar chart illustrates the contribution of each habitat to the Recommended Nutrient Intake (RNI) for six fundamental nutrients, based on a 100g portion. Each bar is a color-segmented stacked visual, with distinct hues corresponding to individual nutrients, and white numbers within indicating the specific percentage contribution of each nutrient." width="864" />
+<div class="figure"><span style="display:block;" id="fig:unnamed-chunk-5"></span>
+<img src="Timor-nutrient-sensitive-fisheries-management_files/figure-html/unnamed-chunk-5-1.png" alt="Nutritional and economic profiling of key fish groups within the Timor-Leste fishery.Panel A, Distribution of nutritional content among different functional fish groups: Small pelagics, Large pelagics, Small demersals, Large demersals, Sharks and rays and Other groups, that includes shrimps, molluscs, cephalopods and crustaceans. The plot shows the ranked contribution of each functional fish to the supply of calcium, omega-3, iron, protein, vitamin A, and zinc during the period 2018-2023. Panel B, Comparative analysis of nutritional score versus economic accessibility for key fish groups. This scatter plot displays the relationship between the cumulative nutritional score and the market price for various fish groups within Timor-Leste fishery. The x-axis quantifies the cumulative contribution to the Recommended Nutrient Intake (RNI) for six essential nutrients (zinc, protein, omega-3, calcium, iron, vitamin A) from a 100g portion of each fish group. The y-axis represents the average market price per kilogram for each group. Dot size and the accompanying numerical labels reflect the relative catch percentage of each group, serving as an index of accessibility and availability. Panel C, The bar chart illustrates the contribution of each habitat to the Recommended Nutrient Intake (RNI) for six fundamental nutrients, based on a 100g portion. Each bar is a color-segmented stacked visual, with distinct hues corresponding to individual nutrients, and white numbers within indicating the specific percentage contribution of each nutrient." width="864" />
 <p class="caption">
 Figure 4.3: Nutritional and economic profiling of key fish groups within the Timor-Leste fishery.Panel A, Distribution of nutritional content among different functional fish groups: Small pelagics, Large pelagics, Small demersals, Large demersals, Sharks and rays and Other groups, that includes shrimps, molluscs, cephalopods and crustaceans. The plot shows the ranked contribution of each functional fish to the supply of calcium, omega-3, iron, protein, vitamin A, and zinc during the period 2018-2023. Panel B, Comparative analysis of nutritional score versus economic accessibility for key fish groups. This scatter plot displays the relationship between the cumulative nutritional score and the market price for various fish groups within Timor-Leste fishery. The x-axis quantifies the cumulative contribution to the Recommended Nutrient Intake (RNI) for six essential nutrients (zinc, protein, omega-3, calcium, iron, vitamin A) from a 100g portion of each fish group. The y-axis represents the average market price per kilogram for each group. Dot size and the accompanying numerical labels reflect the relative catch percentage of each group, serving as an index of accessibility and availability. Panel C, The bar chart illustrates the contribution of each habitat to the Recommended Nutrient Intake (RNI) for six fundamental nutrients, based on a 100g portion. Each bar is a color-segmented stacked visual, with distinct hues corresponding to individual nutrients, and white numbers within indicating the specific percentage contribution of each nutrient.
 </p>

docs/index.html

@@ -143,7 +143,7 @@ <h1>
 <div id="header">
 <h1 class="title">Modelling scenarios for nutrient-sensitive fisheries management</h1>
 <p class="author"><em>Lorenzo Longobardi</em></p>
-<p class="date"><em>Last update: 2024-05-25</em></p>
+<p class="date"><em>Last update: 2024-05-26</em></p>
 </div>
 <div id="content" class="section level1 hasAnchor" number="1">
 <h1><span class="header-section-number">1</span> Content<a href="index.html#content" class="anchor-section" aria-label="Anchor link to header"></a></h1>