508 continued

almost there

documents/nca/62appendix_crfs_onboard.Rmd

@@ -201,6 +201,7 @@ sa4ss::add_figure(
 filein = file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",
                    "deltalogn", "index.png"), 
 caption = "Index for the onboard CPFV survey.",
+alt_caption = "Index for the CPFV survey indicating a flat index until 2016 when the relative index indreases.",
 label = 'onboard-index')
 ```
 
@@ -211,6 +212,7 @@ sa4ss::add_figure(
 filein = file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",
                    "deltalogn", "qq.png"), 
 caption = "Q-Q plot for the onboard CPFV survey.",
+alt_caption = "The q q plot shows a decent fit to the data.",
 label = 'onboard-qq')
 ```
 
@@ -222,6 +224,7 @@ sa4ss::add_figure(
 filein = file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",
                    "average_cpue_by_district.png"), 
 caption = "Average CPUE by district prior to standardization.",
+alt_caption = "Average CPUE by district whosing that the trends across district are similar.",
 label = 'onboard-regioncpue')
 ```
 
@@ -232,6 +235,7 @@ sa4ss::add_figure(
 filein = file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",
                    "copper_depths_gisdepthadded.png"), 
 caption = "Distribution by year of depths where copper rockfish observed.",
+alt_caption = "Distribution of depths showing an increase in the mean as you move through time",
 label = 'onboard-depths')
 ```
 
@@ -243,6 +247,7 @@ sa4ss::add_figure(
 filein = file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",
                    "drifts_by_depth_district.png"), 
 caption = "Depths of observed copper rockfish by district.",
+alt_caption = "Number of drifts with copper rockfish by depth indicating copper rockfish are mostly found shallower than 300 feet.",
 label = 'onboard-depths2')
 ```
 

documents/nca/64appendix_crfs_dockside.Rmd

@@ -205,6 +205,7 @@ sa4ss::add_figure(
   caption = "Distribution by year of the number of copper rockfish retained per angler. 
   This includes sampler observed and angler reported catch. The vertical line at 1 represents the sub-bag 
   limit implemented in 2022.",
+  alt_caption = "The number of copper rockfish retained did not significanly change with the changing bag limits",
   label = "pr-bag"
 )
 ```
@@ -218,6 +219,7 @@ sa4ss::add_figure(
     "average_cpue_by_cnty.png"
   ),
   caption = "Average CPUE by district prior to standardization.",
+    alt_caption = "The average CPUE by district shows a trend of increasing average CPUE and higher CPUE in district four.",
   label = "pr-districtcpue"
 )
 ```
@@ -232,6 +234,7 @@ sa4ss::add_figure(
     "index.png"
   ),
   caption = "Index for the dockside PR survey.",
+    alt_caption = "The index is relatively flat until an increase in 2015.",
   label = "pr-index"
 )
 ```
@@ -245,6 +248,7 @@ sa4ss::add_figure(
     "rm_last2yrs_area_weighted", "negbin_prop_zero_main_effects.png"
   ),
   caption = "Predicted proportion of zeroes from the Bayesian fit to the main effects model.",
+    alt_caption = "The predicted proportion of zeroes is within 0.5% of the data.",
   label = "pr-prop-zero"
 )
 ```
@@ -261,6 +265,7 @@ sa4ss::add_figure(
     "rm_last2yrs_area_weighted", "qq.png"
   ),
   caption = "Q-Q plot for the dockside PR survey.",
+    alt_caption = "The qq plot indicates a relatively good fit with some diversion of the 1:1 line on the upper quantiles.",
   label = "pr-qq"
 )
 ```

documents/nca/65appendix_ccfrp.Rmd

@@ -111,6 +111,7 @@ sa4ss::table_format(x = ind,
 sa4ss::add_figure(
 filein = file.path(data_dir, "survey_indices", "ccfrp", "north", "mpa_site_cpue.png"), 
 caption = "Average CPUE by site with trends prior to standardization in the MPA and REF areas.",
+alt_caption = "The average CPUE is higher in the MPAs at Piedras Blancas, Point Lobos and Stewarts Point.",
 label = 'ccfrp-avg-cpue')
 ```
 
@@ -119,6 +120,7 @@ label = 'ccfrp-avg-cpue')
 sa4ss::add_figure(
 filein = file.path(data_dir, "survey_indices", "ccfrp", "north", "area_weighted", "qq.png"), 
 caption = "QQ-plot for the CCFRP survey.",
+alt_caption = "The q q plots indicates a fairly good fit to the index.",
 label = 'ccfrp-qq')
 ```
 
@@ -129,7 +131,7 @@ label = 'ccfrp-qq')
 sa4ss::add_figure(
 filein = file.path(data_dir, "survey_indices", "ccfrp", "north", "area_weighted", "Index.png"), 
 caption = "The weighted relative index of abundance.",
+alt_caption = "The weighted index is relatively flat until 2015 and then increases.",
 label = 'ccfrp-index')
 ```
 
-

documents/nca/70appendix_cpfv.Rmd

@@ -32,7 +32,7 @@ From the onboard observer trips in District 1, 37 percent of the observed copper
 
 In District 2, 17 percent of the observed copper rockfish were from half-day day trips, 75 percent from the three-quarter to full day trips, and 8 percent from multi-day trips. When weather allows, the northern Channel Islands can be accessed from CRFS District 2 during a three-quarter to full-day trip or a multi-day trip, depending on the port. For instance, the CPFVs from Channel Islands Sportfishing in Oxnard, California access the northern Channel Islands during multi-day trips, and the same areas are accessed by the three-quarter to full-day trips out of Santa Barbara Landing. 
 
-The majority of length samples for the CPFV fleet are taken onboard the observed trips. The shift in the distribution of lengths from each trip type is evident from the overnight trips from District 1 with larger fish encountered on the overnight trips (Figure \ref{fig:copper-lengths}.  The average length of fish encountered on half-day trips out of District 2 is 33.1 cm compared to 36.3 for three-quarter day trips and 36.6 for overnight trips.  
+The majority of length samples for the CPFV fleet are taken onboard the observed trips. The shift in the distribution of lengths from each trip type is evident from the overnight trips from District 1 with larger fish encountered on the overnight trips (Figure \ref{fig:copper-lengths}).  The average length of fish encountered on half-day trips out of District 2 is 33.1 cm compared to 36.3 for three-quarter day trips and 36.6 for overnight trips.  
 
 To account for the differences in the the differences in catch rates and size compositions observed across trip types and areas, we would need to collect estimates of catch and effort at a finer-scale than the CRFS district. While the logbooks are not perfect, and there is a fraction of non-compliance, they highlight the intense fishing pressure in some areas and may help identify the how to distribute sampling efforts. For example, increased sampling in Districts 4-6 would also provide information on the length composition of the fish encountered by the CPFV fleet, especially considering the increase in average length with latitude (Figure \@ref(fig:copper-lengths)). The increased sampling in District 4-6 would also provide the data needed to create an accurate index of relative abundance from the onboard observer data, which can easily be considered one of the most valuable fishery-dependent data sources available. Based on additional data from the logbooks it may be possible to identify an approximate fraction of half-day to three-quarter day trips.
 The lengths in Table \@ref(tab:copper-lengths) are currently all weighted equally in the length compositions within the current assessment models. Future research is needed to determine the effects of the changing size composition by trip type within stock assessment models, especially for southern California where larger fish are encountered on longer trips. Weighting the length composition data by the catch from each trip type is one possible method to account for the differences observed in Figure \@ref(fig:copper-lengths). 
@@ -44,6 +44,7 @@ The lengths in Table \@ref(tab:copper-lengths) are currently all weighted equall
 sa4ss::add_figure(
 filein = file.path(data_dir, "rec_indices", "cpfv_logbook_summaries", "crfs_districts.png"), 
 caption = "Map of the CDFW CRFS sampling Districts.",
+alt_caption = "A map showing the six sampling districts, with district one and two south of Point Conception.",
 label = 'crfs-districts')
 ```
 
@@ -53,6 +54,7 @@ label = 'crfs-districts')
 sa4ss::add_figure(
 filein = file.path(data_dir, "rec_indices", "cpfv_logbook_summaries", "length_by_triptype.png"), 
 caption = "Distribution of the lengths of copper rockfish measured from 2018-2019 from dockside angler interviews by district.",
+alt_caption = "The length distribution of copper rockfish encountered on overnight trips is larger than on single day trips.",
 label = 'copper-lengths')
 ```