Merge branch 'gh-pages' of https://github.com/OHI-Science/ohiprep_v2024…

… into gh-pages

globalprep/ao/v2024/ao_stock_status_saup.Rmd

@@ -43,15 +43,15 @@ For v2023 and v2024 the Sea Around us Project (SAUP) data used in the ao_catch_p
 **Additional Information**: [Methods](http://www.seaaroundus.org/sea-around-us-methods-index/)
 
 
-**Reference**: [RAM Legacy Stock Assessment Database](http://ramlegacy.org) v4.495
+**Reference**: [RAM Legacy Stock Assessment Database](http://ramlegacy.org) v4.65
 
-**Downloaded**: 07/06/2023
+**Downloaded**: 08/07/2024
 
 **Description**: B/Bmsy value by stock and year (other data, which we do not use, are also available in the database)
 
 **Native data resolution**: stock (fish stock, species and region specific)
 
-**Time range**: 1800 - 2022 (we only use the year which matches our fisheries catch data (2019 for v2023))
+**Time range**: 1800 - 2023 (we only use the year which matches our fisheries catch data (2019 for v2024))
 
 **Format**: CSV format 
 
@@ -286,7 +286,7 @@ compare <- new %>%
 ```
 
 
-```{r, eval = FALSE}
+```{r, eval=FALSE}
 library(plotly)
 library(ggplot2)
 
@@ -299,16 +299,13 @@ compare_plotly <- ggplotly(compare_plot, tooltip = c("text", "score", "old_score
 compare_plotly
 
 htmlwidgets::saveWidget(compare_plotly, here::here("globalprep","ao", version_year, "figs","v2023_v2024_compare_plot.html"))
-```
 
-```{r}
-library(tidyverse)
-library(here)
-library(htmlwidgets)
-library(patchwork)
-library(ggplot2)
-library(dplyr)
-source(here("workflow", "R", "common.R"))
+#look at the difference between this year and last
+new <- read_csv(here::here("globalprep","ao",version_year, "output","ao_nind_scores.csv")) %>%
+  left_join(rgns_eez)
+
+old <- read_csv(here::here("globalprep","ao",previous_version_year, "output","ao_nind_scores.csv")) %>% 
+  select(rgn_id, year, old_score = score)
 
 # ==== Percent change between this year and last year =====
 compare_diff <- new %>% 
@@ -367,7 +364,7 @@ patch_rgn_3
 # saveWidget(patch_rgn_3, here::here("globalprep","ao", version_year, "figs","rgn_3_score_comparison.html"))
 ```
 
-```{r echo=TRUE}
+```{r, eval = FALSE}
 
 region_data() # to have access to rgns_all and rgns_eez
 

globalprep/fis/v2024/STEP1_download_saup_match_fao_data_fix.html

@@ -9,7 +9,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 
-<meta name="author" content="Compiled on Wed Aug 14 16:30:15 2024 by lecuona" />
+<meta name="author" content="Compiled on Wed Sep 4 16:58:27 2024 by lecuona" />
 
 
 <title>OHI 2024: Download SAUP production data and match FAO regions</title>
@@ -1647,7 +1647,7 @@
 
 <h1 class="title toc-ignore">OHI 2024: Download SAUP production data and
 match FAO regions</h1>
-<h4 class="author"><em>Compiled on Wed Aug 14 16:30:15 2024 by
+<h4 class="author"><em>Compiled on Wed Sep 4 16:58:27 2024 by
 lecuona</em></h4>
 
 </div>

globalprep/fis/v2024/STEP2a_saup_catch_prep.html

@@ -9,7 +9,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 
-<meta name="author" content="Compiled on Wed Aug 14 16:31:25 2024 by lecuona" />
+<meta name="author" content="Compiled on Wed Sep 4 17:00:06 2024 by lecuona" />
 
 
 <title>OHI 2024: Food Provision, Preparing catch data for BBmsy calculations and mean catch (weights in FIS model) and FP weights</title>
@@ -1648,7 +1648,7 @@
 <h1 class="title toc-ignore">OHI 2024: Food Provision, Preparing catch
 data for BBmsy calculations and mean catch (weights in FIS model) and FP
 weights</h1>
-<h4 class="author"><em>Compiled on Wed Aug 14 16:31:25 2024 by
+<h4 class="author"><em>Compiled on Wed Sep 4 17:00:06 2024 by
 lecuona</em></h4>
 
 </div>

globalprep/fis/v2024/STEP2b_species_resilience_lookup_table.Rmd

@@ -3,14 +3,19 @@ title: "OHI 2024: FP, SAUP Species Resilience Lookup Table"
 author: "*Compiled on `r date()` by `r Sys.info()['user']`*"
 output: 
   html_document:
-  toc: true
-number_sections: true
-theme: cerulean
-highlight: haddock
-includes: 
-  in_header: '../../../workflow/templates/ohi_hdr.html'
+    code_folding: show
+    toc: true
+    toc_depth: 1
+    toc_float: yes
+    number_sections: false
+    theme: cerulean
+    highlight: haddock
+    includes: 
+      in_header: '../../../workflow/templates/ohi_hdr.html'
 pdf_document:
   toc: true
+editor_options: 
+  chunk_output_type: console
 ---
 
 # Summary
@@ -23,11 +28,12 @@ This script uses FishBase to find the Resilience for each of the species in the
 
 # Setup
 
-```{r setup, include=FALSE}
+```{r setup, include=FALSE, eval = FALSE}
 
 knitr::opts_chunk$set(echo = TRUE, eval=FALSE)
 
 library(dplyr)
+# install.packages("rfishbase", repos = "http://cran.us.r-project.org")
 library(rfishbase)
 library(parallel)
 

globalprep/fis/v2024/STEP3_calculate_bbmsy.html

@@ -9,10 +9,10 @@
 <meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 
-<meta name="author" content="Compiled on Mon Sep 11 08:22:41 2023 by egg" />
+<meta name="author" content="Compiled on Wed Sep 4 17:07:06 2024 by lecuona" />
 
 
-<title>OHI 2023: Food Provision, Calculating fisheries stock status</title>
+<title>OHI 2024: Food Provision, Calculating fisheries stock status</title>
 
 <script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
 // be compatible with the behavior of Pandoc < 2.8).
@@ -1378,7 +1378,7 @@
 </style>
 <style type="text/css" data-origin="pandoc">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -1645,10 +1645,10 @@
 
 
 
-<h1 class="title toc-ignore">OHI 2023: Food Provision, Calculating
+<h1 class="title toc-ignore">OHI 2024: Food Provision, Calculating
 fisheries stock status</h1>
-<h4 class="author"><em>Compiled on Mon Sep 11 08:22:41 2023 by
-egg</em></h4>
+<h4 class="author"><em>Compiled on Wed Sep 4 17:07:06 2024 by
+lecuona</em></h4>
 
 </div>
 
@@ -1667,8 +1667,8 @@ <h1>Summary</h1>
 <div id="updates-from-previous-scenario-year" class="section level1">
 <h1>Updates from previous scenario year</h1>
 <ul>
-<li>None. This script wasn’t run in v2023. Associated data files within
-the repo were copied from v2022 to v2023.</li>
+<li>None. This script wasn’t run in v2024. Associated data files within
+the repo were copied from v2023 to v2024.</li>
 </ul>
 </div>
 <div id="setup" class="section level1">
@@ -1684,10 +1684,7 @@ <h1>Setup</h1>
 <span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a><span class="fu">library</span>(doParallel)</span>
 <span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a><span class="fu">library</span>(here)</span>
 <span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a></span>
-<span id="cb2-9"><a href="#cb2-9" tabindex="-1"></a><span class="fu">setwd</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;globalprep/fis/v2022&quot;</span>))</span>
-<span id="cb2-10"><a href="#cb2-10" tabindex="-1"></a></span>
-<span id="cb2-11"><a href="#cb2-11" tabindex="-1"></a></span>
-<span id="cb2-12"><a href="#cb2-12" tabindex="-1"></a><span class="fu">source</span>(<span class="fu">here</span>(<span class="st">&#39;workflow/R/common.R&#39;</span>))</span></code></pre></div>
+<span id="cb2-9"><a href="#cb2-9" tabindex="-1"></a><span class="fu">source</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;workflow&quot;</span>, <span class="st">&quot;R&quot;</span>, <span class="st">&quot;common.R&quot;</span>)) <span class="co"># file creates objects to process data</span></span></code></pre></div>
 </div>
 <div id="load-catch-data" class="section level1">
 <h1>Load catch data</h1>