clean up plot title

docs/search.json

@@ -249,7 +249,7 @@
     "href": "tutorial/Mackenzie_SDM_with_maxent.html#visualization",
     "title": "Maxent SDM attempt",
     "section": "Visualization",
-    "text": "Visualization\n\n# ggplot - with occurrence data points\n\nggplot() +\n  geom_stars(data = predicted) +\n  scale_fill_cmocean(name = \"ice\", direction = -1, guide = guide_colorbar(barwidth = 1, barheight = 10, ticks = FALSE, nbin = 1000, frame.colour = \"black\"), limits = c(0, 1)) +\n  theme_linedraw() +\n  theme(panel.background = element_blank(),\n        panel.grid.major = element_blank(),\n        panel.grid.minor = element_blank()) +\n  labs(title = \"Loggerhead and green sea turtle species distribution model in the Arabian Sea\",\n       x = \"Longitude\",\n       y = \"Latitude\",\n       fill = \"Probability\",\n       shape = \"Species (presence)\",\n       subtitle = \"Environmental predictors: mean SS temp, mean SS salinity, mean bathymetry, \\nmean pH, mean DO, mean SS chlorophyll-a, mean SS nitrate\") +\n  geom_point(occ.points, mapping = aes(shape = common.name, geometry = geometry), stat = \"sf_coordinates\", alpha = 0.3, color = \"purple\") +\n  #scale_x_continuous(breaks = seq(40, 70, 10), limits = c(42, 70))+\n  scale_y_continuous(breaks = seq(0, 30, 10))\n\n\n\nggsave(\"SDM_loggerhead_green_w points.pdf\", height = 6, width = 8.5)\n\n\n# ggplot - without occurrence data points\n\nggplot() +\n  geom_stars(data = predicted) +\n  scale_fill_cmocean(name = \"ice\", direction = -1, guide = guide_colorbar(barwidth = 1, barheight = 10, ticks = FALSE, nbin = 1000, frame.colour = \"black\"), limits = c(0, 1)) +\n  theme_linedraw() +\n  theme(panel.background = element_blank(),\n        panel.grid.major = element_blank(),\n        panel.grid.minor = element_blank()) +\n  labs(title = \"Loggerhead and green sea turtle species distribution model in the Arabian Sea\",\n       x = \"Longitude\",\n       y = \"Latitude\",\n       fill = \"Probability\",\n       shape = \"Species (presence)\",\n       subtitle = \"Environmental predictors: mean SS temp, mean SS salinity, mean bathymetry,\\nmean pH, mean DO, mean SS chlorophyll-a, mean SS nitrate\") +\n  #geom_point(occ.points, mapping = aes(shape = common.name, geometry = geometry), stat = \"sf_coordinates\", alpha = 0.3, color = \"purple\") +\n  #scale_x_continuous(breaks = seq(40, 70, 10), limits = c(42, 70))+\n  scale_y_continuous(breaks = seq(0, 30, 10))\n\n\n\nggsave(\"SDM_loggerhead_green.pdf\", height = 6, width = 8.5)\n\n\n# ggplot - with occurrence and absence data points\n\nggplot() +\n  geom_stars(data = predicted) +\n  scale_fill_cmocean(name = \"ice\", direction = -1, guide = guide_colorbar(barwidth = 1, barheight = 10, ticks = FALSE, nbin = 1000, frame.colour = \"black\"), limits = c(0, 1)) +\n  theme_linedraw() +\n  theme(panel.background = element_blank(),\n        panel.grid.major = element_blank(),\n        panel.grid.minor = element_blank()) +\n  labs(title = \"Loggerhead and green sea turtle species distribution model in the Arabian Sea\",\n       x = \"Longitude\",\n       y = \"Latitude\",\n       fill = \"Probability\",\n       shape = \"Species (presence)\",\n       subtitle = \"Environmental predictors: mean SS temp, mean SS salinity, mean bathymetry, \\nmean pH, mean DO, mean SS chlorophyll-a, mean SS nitrate\") +\n  geom_point(occ.points, mapping = aes(shape = common.name, geometry = geometry), stat = \"sf_coordinates\", alpha = 0.3, color = \"purple\") +\n  #scale_x_continuous(breaks = seq(40, 70, 10), limits = c(42, 70))+\n  scale_y_continuous(breaks = seq(0, 30, 10)) +\n  geom_point(abs.points, mapping = aes(geometry = geometry), stat = \"sf_coordinates\", alpha = 0.3, color = \"green\") # adding in absence data"
+    "text": "Visualization\n\n# ggplot - with occurrence data points\n\nggplot() +\n  geom_stars(data = predicted) +\n  scale_fill_cmocean(name = \"ice\", direction = -1, guide = guide_colorbar(barwidth = 1, barheight = 10, ticks = FALSE, nbin = 1000, frame.colour = \"black\"), limits = c(0, 1)) +\n  theme_linedraw() +\n  theme(panel.background = element_blank(),\n        panel.grid.major = element_blank(),\n        panel.grid.minor = element_blank()) +\n  labs(title = \"Loggerhead and green sea turtle SDM in the Arabian Sea\",\n       x = \"Longitude\",\n       y = \"Latitude\",\n       fill = \"Probability\",\n       shape = \"Species (presence)\",\n       subtitle = \"Environmental predictors: mean SS temp, mean SS salinity, mean bathymetry, \\nmean pH, mean DO, mean SS chlorophyll-a, mean SS nitrate\") +\n  geom_point(occ.points, mapping = aes(shape = common.name, geometry = geometry), stat = \"sf_coordinates\", alpha = 0.3, color = \"purple\") +\n  #scale_x_continuous(breaks = seq(40, 70, 10), limits = c(42, 70))+\n  scale_y_continuous(breaks = seq(0, 30, 10))\n\n\n\nggsave(\"SDM_loggerhead_green_w points.pdf\", height = 6, width = 8.5)\n\n\n# ggplot - without occurrence data points\n\nggplot() +\n  geom_stars(data = predicted) +\n  scale_fill_cmocean(name = \"ice\", direction = -1, guide = guide_colorbar(barwidth = 1, barheight = 10, ticks = FALSE, nbin = 1000, frame.colour = \"black\"), limits = c(0, 1)) +\n  theme_linedraw() +\n  theme(panel.background = element_blank(),\n        panel.grid.major = element_blank(),\n        panel.grid.minor = element_blank()) +\n  labs(title = \"Loggerhead and green sea turtle SDM in the Arabian Sea\",\n       x = \"Longitude\",\n       y = \"Latitude\",\n       fill = \"Probability\",\n       shape = \"Species (presence)\",\n       subtitle = \"Environmental predictors: mean SS temp, mean SS salinity, mean bathymetry,\\nmean pH, mean DO, mean SS chlorophyll-a, mean SS nitrate\") +\n  #geom_point(occ.points, mapping = aes(shape = common.name, geometry = geometry), stat = \"sf_coordinates\", alpha = 0.3, color = \"purple\") +\n  #scale_x_continuous(breaks = seq(40, 70, 10), limits = c(42, 70))+\n  scale_y_continuous(breaks = seq(0, 30, 10))\n\n\n\nggsave(\"SDM_loggerhead_green.pdf\", height = 6, width = 8.5)\n\n\n# ggplot - with occurrence and absence data points\n\nggplot() +\n  geom_stars(data = predicted) +\n  scale_fill_cmocean(name = \"ice\", direction = -1, guide = guide_colorbar(barwidth = 1, barheight = 10, ticks = FALSE, nbin = 1000, frame.colour = \"black\"), limits = c(0, 1)) +\n  theme_linedraw() +\n  theme(panel.background = element_blank(),\n        panel.grid.major = element_blank(),\n        panel.grid.minor = element_blank()) +\n  labs(title = \"Loggerhead and green sea turtle SDM in the Arabian Sea\",\n       x = \"Longitude\",\n       y = \"Latitude\",\n       fill = \"Probability\",\n       shape = \"Species (presence)\",\n       subtitle = \"Environmental predictors: mean SS temp, mean SS salinity, mean bathymetry, \\nmean pH, mean DO, mean SS chlorophyll-a, mean SS nitrate\") +\n  geom_point(occ.points, mapping = aes(shape = common.name, geometry = geometry), stat = \"sf_coordinates\", alpha = 0.3, color = \"purple\") +\n  #scale_x_continuous(breaks = seq(40, 70, 10), limits = c(42, 70))+\n  scale_y_continuous(breaks = seq(0, 30, 10)) +\n  geom_point(abs.points, mapping = aes(geometry = geometry), stat = \"sf_coordinates\", alpha = 0.3, color = \"green\") # adding in absence data"
   },
   {
     "objectID": "tutorial/Roadmap.html",

docs/sitemap.xml

@@ -2,50 +2,50 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>https://oceanhackweek.org/index.html</loc>
-    <lastmod>2023-08-11T17:21:13.223Z</lastmod>
+    <lastmod>2023-08-11T17:30:29.961Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/00_Roadmap.html</loc>
-    <lastmod>2023-08-11T17:21:14.459Z</lastmod>
+    <lastmod>2023-08-11T17:30:31.157Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/01_Presence_Data.html</loc>
-    <lastmod>2023-08-11T17:21:15.371Z</lastmod>
+    <lastmod>2023-08-11T17:30:32.023Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/02_Background_Data.html</loc>
-    <lastmod>2023-08-11T17:21:16.417Z</lastmod>
+    <lastmod>2023-08-11T17:30:33.104Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/03_sdmpredictors-variables.html</loc>
-    <lastmod>2023-08-11T17:21:17.398Z</lastmod>
+    <lastmod>2023-08-11T17:30:34.104Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/04_models.html</loc>
-    <lastmod>2023-08-11T17:21:17.901Z</lastmod>
+    <lastmod>2023-08-11T17:30:34.621Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/Mackenzie_SDM_with_maxent.html</loc>
-    <lastmod>2023-08-11T17:22:10.877Z</lastmod>
+    <lastmod>2023-08-11T17:30:35.571Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/Roadmap.html</loc>
-    <lastmod>2023-08-11T17:22:11.400Z</lastmod>
+    <lastmod>2023-08-11T17:30:36.066Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/background.html</loc>
-    <lastmod>2023-08-11T17:22:12.211Z</lastmod>
+    <lastmod>2023-08-11T17:30:36.905Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/maxent-sdm.html</loc>
-    <lastmod>2023-08-11T17:22:13.021Z</lastmod>
+    <lastmod>2023-08-11T17:30:37.700Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/occ_env.html</loc>
-    <lastmod>2023-08-11T17:22:13.832Z</lastmod>
+    <lastmod>2023-08-11T17:30:38.494Z</lastmod>
   </url>
   <url>
     <loc>https://oceanhackweek.org/tutorial/seaturtle_robis.html</loc>
-    <lastmod>2023-08-11T17:22:14.591Z</lastmod>
+    <lastmod>2023-08-11T17:30:39.234Z</lastmod>
   </url>
 </urlset>

docs/tutorial/Mackenzie_SDM_with_maxent.html

@@ -610,7 +610,7 @@ <h2 class="anchored" data-anchor-id="visualization">Visualization</h2>
 <span id="cb45-7"><a href="#cb45-7" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme</span>(<span class="at">panel.background =</span> <span class="fu">element_blank</span>(),</span>
 <span id="cb45-8"><a href="#cb45-8" aria-hidden="true" tabindex="-1"></a>        <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
 <span id="cb45-9"><a href="#cb45-9" aria-hidden="true" tabindex="-1"></a>        <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
-<span id="cb45-10"><a href="#cb45-10" aria-hidden="true" tabindex="-1"></a>  <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Loggerhead and green sea turtle species distribution model in the Arabian Sea"</span>,</span>
+<span id="cb45-10"><a href="#cb45-10" aria-hidden="true" tabindex="-1"></a>  <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Loggerhead and green sea turtle SDM in the Arabian Sea"</span>,</span>
 <span id="cb45-11"><a href="#cb45-11" aria-hidden="true" tabindex="-1"></a>       <span class="at">x =</span> <span class="st">"Longitude"</span>,</span>
 <span id="cb45-12"><a href="#cb45-12" aria-hidden="true" tabindex="-1"></a>       <span class="at">y =</span> <span class="st">"Latitude"</span>,</span>
 <span id="cb45-13"><a href="#cb45-13" aria-hidden="true" tabindex="-1"></a>       <span class="at">fill =</span> <span class="st">"Probability"</span>,</span>
@@ -634,7 +634,7 @@ <h2 class="anchored" data-anchor-id="visualization">Visualization</h2>
 <span id="cb47-7"><a href="#cb47-7" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme</span>(<span class="at">panel.background =</span> <span class="fu">element_blank</span>(),</span>
 <span id="cb47-8"><a href="#cb47-8" aria-hidden="true" tabindex="-1"></a>        <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
 <span id="cb47-9"><a href="#cb47-9" aria-hidden="true" tabindex="-1"></a>        <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
-<span id="cb47-10"><a href="#cb47-10" aria-hidden="true" tabindex="-1"></a>  <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Loggerhead and green sea turtle species distribution model in the Arabian Sea"</span>,</span>
+<span id="cb47-10"><a href="#cb47-10" aria-hidden="true" tabindex="-1"></a>  <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Loggerhead and green sea turtle SDM in the Arabian Sea"</span>,</span>
 <span id="cb47-11"><a href="#cb47-11" aria-hidden="true" tabindex="-1"></a>       <span class="at">x =</span> <span class="st">"Longitude"</span>,</span>
 <span id="cb47-12"><a href="#cb47-12" aria-hidden="true" tabindex="-1"></a>       <span class="at">y =</span> <span class="st">"Latitude"</span>,</span>
 <span id="cb47-13"><a href="#cb47-13" aria-hidden="true" tabindex="-1"></a>       <span class="at">fill =</span> <span class="st">"Probability"</span>,</span>
@@ -658,7 +658,7 @@ <h2 class="anchored" data-anchor-id="visualization">Visualization</h2>
 <span id="cb49-7"><a href="#cb49-7" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme</span>(<span class="at">panel.background =</span> <span class="fu">element_blank</span>(),</span>
 <span id="cb49-8"><a href="#cb49-8" aria-hidden="true" tabindex="-1"></a>        <span class="at">panel.grid.major =</span> <span class="fu">element_blank</span>(),</span>
 <span id="cb49-9"><a href="#cb49-9" aria-hidden="true" tabindex="-1"></a>        <span class="at">panel.grid.minor =</span> <span class="fu">element_blank</span>()) <span class="sc">+</span></span>
-<span id="cb49-10"><a href="#cb49-10" aria-hidden="true" tabindex="-1"></a>  <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Loggerhead and green sea turtle species distribution model in the Arabian Sea"</span>,</span>
+<span id="cb49-10"><a href="#cb49-10" aria-hidden="true" tabindex="-1"></a>  <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Loggerhead and green sea turtle SDM in the Arabian Sea"</span>,</span>
 <span id="cb49-11"><a href="#cb49-11" aria-hidden="true" tabindex="-1"></a>       <span class="at">x =</span> <span class="st">"Longitude"</span>,</span>
 <span id="cb49-12"><a href="#cb49-12" aria-hidden="true" tabindex="-1"></a>       <span class="at">y =</span> <span class="st">"Latitude"</span>,</span>
 <span id="cb49-13"><a href="#cb49-13" aria-hidden="true" tabindex="-1"></a>       <span class="at">fill =</span> <span class="st">"Probability"</span>,</span>

tutorial/Mackenzie_SDM_with_maxent.Rmd

@@ -184,7 +184,7 @@ ggplot() +
   theme(panel.background = element_blank(),
         panel.grid.major = element_blank(),
         panel.grid.minor = element_blank()) +
-  labs(title = "Loggerhead and green sea turtle species distribution model in the Arabian Sea",
+  labs(title = "Loggerhead and green sea turtle SDM in the Arabian Sea",
        x = "Longitude",
        y = "Latitude",
        fill = "Probability",
@@ -208,7 +208,7 @@ ggplot() +
   theme(panel.background = element_blank(),
         panel.grid.major = element_blank(),
         panel.grid.minor = element_blank()) +
-  labs(title = "Loggerhead and green sea turtle species distribution model in the Arabian Sea",
+  labs(title = "Loggerhead and green sea turtle SDM in the Arabian Sea",
        x = "Longitude",
        y = "Latitude",
        fill = "Probability",
@@ -232,7 +232,7 @@ ggplot() +
   theme(panel.background = element_blank(),
         panel.grid.major = element_blank(),
         panel.grid.minor = element_blank()) +
-  labs(title = "Loggerhead and green sea turtle species distribution model in the Arabian Sea",
+  labs(title = "Loggerhead and green sea turtle SDM in the Arabian Sea",
        x = "Longitude",
        y = "Latitude",
        fill = "Probability",