update fishery indicators with 2024 data pull

.quarto/cites/index.json

@@ -1 +1 @@
-{"Report_book_files\\Report4.qmd":[],"Report_book_files\\Discussion_material.qmd":[],"Report_book_files\\Risk_indicators.qmd":[],"Report_book_files\\FMP_objectives.qmd":[],"Lab-report\\OA.qmd":[],"index.qmd":[],"Report_book_files\\Intro_text.qmd":[],"Report_book_files\\Performance_indicators.qmd":[],"OA.qmd":[]}
+{"Lab-report\\OA.qmd":[],"Report_book_files\\Intro_text.qmd":[],"Report_book_files\\Report4.qmd":[],"Report_book_files\\Performance_indicators.qmd":[],"Report_book_files\\Risk_indicators.qmd":[],"Report_book_files\\Discussion_material.qmd":[],"OA.qmd":[],"index.qmd":[],"Report_book_files\\FMP_objectives.qmd":[]}

Report_book_files/Performance_indicators.qmd

@@ -1,5 +1,5 @@
 ```{r, message = FALSE, warnings = FALSE}
-devtools::install_github("https://github.com/MandyKarnauskas-NOAA/plotTimeSeries.git")
+#devtools::install_github("https://github.com/MandyKarnauskas-NOAA/plotTimeSeries.git")
 
 library(plotTimeSeries)
 library(spam)
@@ -17,34 +17,31 @@ Indicator 16 - abundance of economically important fish
 
 ```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/RVC_PR.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
+plotIndicatorTimeSeries(ind, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
 ```
 
 ```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/RVC_STSJ.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
+plotIndicatorTimeSeries(ind, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
 ```
 
 ```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/RVC_STX.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
+plotIndicatorTimeSeries(ind, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
 ```
 
-Indicator 16.1 - abundance of commercial fish based on TCRMP and PRCRMP 
-Indicator 16.2 - slope of the size spectrum based on TCRMP and PRCRMP
+Indicator 16.1 - abundance of commercial fish based on TCRMP and PRCRMP Indicator 16.2 - slope of the size spectrum based on TCRMP and PRCRMP
 
 ### Commercial landings
 
 Indicator 17
 
-```{r, message = FALSE, warnings = FALSE}
-load("../indicator_objects/landings.RData")
+load("../indicator_objects/landings.RData") 
 plotIndicatorTimeSeries(inddata, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
-```
 
 ```{r}
 load("../indicator_objects/fish_density.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, sublabel = T)
+plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, sublabel = T)
 ```
 
 ### Pelagic:demersal ratio
@@ -59,18 +56,16 @@ Indicator 19 - Lmax indicator
 
 Indicator 20
 
-```{r, message = FALSE, warnings = FALSE}
-load("../indicator_objects/total_landings.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:9, plotrownum = 3, plotcolnum = 3, trendAnalysis = T, sublabel = T)
-```
+load("../indicator_objects/total_landings.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:9, plotrownum = 3, plotcolnum = 3, trendAnalysis = T, #sublabel = T) 
 
 ## 5.2 Socioeconomic health
 
 ### Total, lobster and conch revenues
 
 Indicator 21 - percent revenues by species group
 
-![](/indicator_plots/per_landings_PR.png) ![](/indicator_plots/per_landings_STT.png) ![](/indicator_plots/per_ landings_STX.png)
+![](/indicator_plots/per_landings_PR.png) ![](/indicator_plots/per_landings_STT.png) ![](/indicator_plots/per_landings_STX.png)
 
 ### Total, lobster and conch trips
 
@@ -80,18 +75,16 @@ Indicator 22 - number of trips
 
 Indicator 23
 
-```{r}
-load("../indicator_objects/OceanNAICS.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:8, plotrownum = 2, trendAnalysis = T, sublabel = T)
-```
+load("../indicator_objects/OceanNAICS.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:8, plotrownum = 2, trendAnalysis = T, sublabel = T) 
 
 ### GDP
 
 Indicator 24
 
 ```{r}
 load("../indicator_objects/GDP.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:2, trendAnalysis = T, sublabel = T)
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = T, sublabel = T)
 ```
 
 ### Unemployment
@@ -100,7 +93,7 @@ Indicator 25
 
 ```{r}
 load("../indicator_objects/unemployment.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:2, trendAnalysis = T, sublabel = T, dateformat = "%Y%b")
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = T, sublabel = T, dateformat = "%Y%b")
 ```
 
 ## 5.3 Equity
@@ -109,10 +102,8 @@ plotIndicatorTimeSeries(inddata, coltoplot = 1:2, trendAnalysis = T, sublabel =
 
 Indicator 26
 
-```{r}
-load("../indicator_objects/gini.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, sublabel = T)
-```
+load("../indicator_objects/gini.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, sublabel = T) 
 
 ### Commercial fishing community engagement and reliance
 
@@ -122,12 +113,10 @@ Indicator 27 - working with Tarsila on
 
 ### Recreational fishing engagement and participation
 
-Indicator 28 
+Indicator 28
 
-```{r, message = FALSE, warnings = FALSE}
-load("../indicator_objects/total_rec_catch.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:2, trendAnalysis = T, sublabel = T)
-```
+load("../indicator_objects/total_rec_catch.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:2, trendAnalysis = T, sublabel = T) 
 
 ### Commercial fishing engagement and participation
 
@@ -161,16 +150,14 @@ Indicator 33
 
 Indicator 34
 
-```{r, message = FALSE, warnings = FALSE}
-load("../indicator_objects/NCRMP_coral_cover_richness.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:6, sublabel = T, trendAnalysis = F)
-```
+load("../indicator_objects/NCRMP_coral_cover_richness.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:6, sublabel = T, trendAnalysis = F) 
 
 ### Coral species diversity
 
 Indicator 35
 
 ```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/coral_spprichness_cover.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:4, sublabel = T, trendAnalysis = T)
+plotIndicatorTimeSeries(ind, coltoplot = 1:4, sublabel = T, trendAnalysis = T)
 ```

Report_book_files/Risk_indicators.qmd

@@ -22,7 +22,7 @@ Indicator 2
 
 ```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/OA.RData")
-plotIndicatorTimeSeries(inddata, trendAnalysis = T)
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
 ```
 
 ### Hurricane activity
@@ -38,39 +38,30 @@ plotIndicatorTimeSeries(ind, trendAnalysis = T)
 
 Indicator 4
 
-```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/turbidity.RData")
-plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, dateformat = "%m-%Y", sublabel = T)
-```
+plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, #dateformat = "%m-%Y", sublabel = T)
 
 ### Sea surface temperature
 
 Indicator 5
 
-```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/Carib_SST.RData")
-plotIndicatorTimeSeries(ind, coltoplot = 1:3, trendAnalysis = T, sublabel = T, dateformat = "%m-%Y")
-```
+plotIndicatorTimeSeries(ind, coltoplot = 1:3, trendAnalysis = T, sublabel = T, #dateformat = "%m-%Y")
 
 ### Marine debris
 
 Indicator 6
 
-```{r, message = FALSE, warnings = FALSE}
-load("../indicator_objects/beach_litter_un_carib.RData")
-plotIndicatorTimeSeries(inddata, trendAnalysis = F)
-```
-
 ```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/marine_debris.RData")
-plotIndicatorTimeSeries(inddata, trendAnalysis = F)
+plotIndicatorTimeSeries(ind, trendAnalysis = F)
 ```
 
 ### Identified point source pollution sites
 
 ```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/pollution.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:2, trendAnalysis = F, sublabel = T)
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = F, sublabel = T)
 ```
 
 ### Primary productivity via ocean color
@@ -99,38 +90,30 @@ plotIndicatorTimeSeries(ind, trendAnalysis = T)
 
 Indicator 11
 
-```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/disturbance.RData")
 plotIndicatorTimeSeries(inddata, coltoplot = 1:3, trendAnalysis = T, sublabel = T)
-```
 
 ### Sargassum inundation
 
 Indicator 12
 
 ```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/Sargassum.RData")
-plotIndicatorTimeSeries(inddata, trendAnalysis = T)
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
 ```
 
-```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/sargassum_innundation_monthly_mean_hu.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:3, sublabel = T, trendAnalysis = T, dateformat = "%Y%b")
-```
+plotIndicatorTimeSeries(inddata, coltoplot = 1:3, sublabel = T, trendAnalysis = T, #dateformat = "%Y%b")
 
 ### Tourism via hotel occupancy
 
 Indicator 13
 
-```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/hotel_occupancy_rates_USVI_and_PR.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:2, sublabel = T, trendAnalysis = T, dateformat = "%Y%b")
-```
+plotIndicatorTimeSeries(inddata, coltoplot = 1:2, sublabel = T, trendAnalysis = T, #dateformat = "%Y%b")
 
-```{r, message = FALSE, warnings = FALSE}
 load("../indicator_objects/hotel_occupancy.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:2, sublabel = T, trendAnalysis = T, dateformat = "%Y%b")
-```
+plotIndicatorTimeSeries(inddata, coltoplot = 1:2, sublabel = T, trendAnalysis = T, #dateformat = "%Y%b")
 
 ### Population change