Finalize rebuilding doc

*Remove appendix B and related text

write_up/ca_rebuilder/00a.Rmd

@@ -3,7 +3,7 @@ month: "`r format(Sys.Date(), '%B')`"
 year: "`r format(Sys.Date(), '%Y')`"
 preamble: |
 csl: canadian-journal-of-fisheries-and-aquatic-sciences.csl
-disclaimer: true
+disclaimer: false
 output:
   sa4ss::techreport_pdf:
     default

write_up/ca_rebuilder/00title.Rmd

@@ -1,3 +1,3 @@
 ---
-title: DRAFT 2023 Rebuilding analysis for quillback rockfish (_Sebastes maliger_) in U.S. waters off the coast of California based on the 2021 stock assessment
+title: 2023 Rebuilding analysis for quillback rockfish (_Sebastes maliger_) in U.S. waters off the coast of California based on the 2021 stock assessment
 ---

write_up/ca_rebuilder/11introduction.Rmd

@@ -2,10 +2,9 @@
 
 The 2021 stock assessment of `r spp` (_`r spp_latin`_) in California waters estimated that the California population of `r spp` in 2021 was below the Minimum Stock Size Threshold (MSST), which is 25$\%$ of unfished spawning output for rockfish stocks [@Langseth_status_2021]. The California population was estimated to have declined below MSST starting in 1992, reached it lowest values in the mid-1990s, increased to near the MSST in the 2000s and early 2010s, and declined in recent years. 
 
-A draft rebuilding analysis was developed in 2021 based on the results of the 2021 assessment [@langseth_rebuild_2022], and was used to inform catch levels (i.e. ACLs) for 2023--2024 using an SPR = 0.55. Subsequently, it was determined that `r spp` was defined in the Groundfish Fishery Management Plan (FMP) as a coastwide stock, so `r spp` in California waters did not meet the criteria for an overfished declaration and a rebuilding plan was not required. Since the 2021 assessment, Amendment 31 to the FMP was approved by the Pacific Fishery Management Council in June 2023, recommending that `r spp` along the U.S. west coast be defined as three separate stocks corresponding to waters off Washington, Oregon, and California [@fed_registry_2023]. Should the recommended change to the FMP be finalized, a determination that the `r spp` stock off California is overfished and in need of rebuilding is expected to follow.
+A draft rebuilding analysis was developed in 2021 based on the results of the 2021 assessment [@langseth_rebuild_2022], and was used to inform catch levels (i.e. ACLs) for 2023--2024 using an SPR = 0.55. Subsequently, it was determined that `r spp` was defined in the Groundfish Fishery Management Plan (FMP) as a coastwide stock, so `r spp` in California waters did not meet the criteria for an overfished declaration and a rebuilding plan was not required. Since the 2021 assessment, Amendment 31 to the FMP was approved by the Pacific Fishery Management Council in June 2023, recommending that `r spp` along the U.S. west coast be defined as three separate stocks corresponding to waters off Washington, Oregon, and California [@fed_registry_2023]. The recommended change to the FMP was finalized in September 2023 and the `r spp` stock off California was declared overfished in December 2023, necessitating an updated rebuilding analysis. 
 
-Given the assumed levels of depletion for `r spp` in California waters and the potential need for rebuilding, a range of alternative rebuilding strategies were examined and are described in this report. This analysis contains updated estimates for removals of `r spp` in California waters in 2021--2024, and applies the alternative rebuilding strategies starting in 2025. 
-<!-- The years by which rebuilding occurred ranged from `r min(reb[[1]]$rebuild_quants$Ttarget)` -- `r max(reb[[2]]$rebuild_quants$Ttarget)` based on various SPR harvest rates from `r round(min(reb[[1]]$rebuild_quants[,2], reb[[2]]$rebuild_quants[,2]), 2)` to `r round(max(reb[[1]]$rebuild_quants[,2], reb[[2]]$rebuild_quants[,2]), 2)` (no harvest). -->
+Given the assumed levels of depletion for `r spp` in California waters and the need for rebuilding, a range of alternative rebuilding strategies were examined and are described in this report. This analysis contains updated estimates for removals of `r spp` in California waters in 2021--2024, and applies the alternative rebuilding strategies starting in 2025. 
 
 
 # Overview of the 2021 stock assessment

write_up/ca_rebuilder/20rebuilding.Rmd

@@ -75,7 +75,5 @@ No current rebuilding plan exists for `r spp` in California waters so the altern
  \item Apply the harvest rate that is estimated to lead to a 50$\%$ probability of recovery by the $\text{T}_\text{MAX}$ from the previous cycle (strategy 6 in TOR).
 \end{itemize}
 
-All of the above rebuilding strategies were conducted assuming removals of `r round(reb[[1]]$acl_matrix[1,2],2)` mt in 2021, `r round(reb[[1]]$acl_matrix[2,2],2)` mt in 2022, `r round(reb[[1]]$acl_matrix[3,2],2)` mt in 2023, and `r round(reb[[1]]$acl_matrix[4,2],2)` mt in 2024, as recommended by the GMT. Results are described in the section below.
-
-At its September 2023 meeting, the Council requested a value of `r round(reb_alt[[1]]$acl_matrix[4,2],2)` mt be used for assumed total removals in 2024. The above rebuilding strategies were rerun incorporating the newly requested value for assumed total removals in 2024. Tables and figures for this additional analysis are provided in [Appendix B](#append_b). 
+All of the above rebuilding strategies were conducted assuming removals of `r round(reb[[1]]$acl_matrix[1,2],2)` mt in 2021, `r round(reb[[1]]$acl_matrix[2,2],2)` mt in 2022, `r round(reb[[1]]$acl_matrix[3,2],2)` mt in 2023, and `r round(reb[[1]]$acl_matrix[4,2],2)` mt in 2024, as recommended by the GMT.
 

write_up/ca_rebuilder/30results.Rmd

@@ -10,5 +10,5 @@ A rebuilding strategy is presented below that includes a rebuilding target year
 
 Summary results from the rebuilding analysis are presented in Table \ref{tab:reb-options}. Within Table \ref{tab:reb-options}, estimated catch values for 2025--2026 from the rebuilding analysis are labeled as ACL values. Detailed results for all runs are presented in Tables \ref{tab:prob-mat}--\ref{tab:rel-ssb-mat} and Figures \ref{fig:prob-fig}--\ref{fig:ssb-fig}. This rebuilding analysis reports results for `r spp` in California waters, and catches can be partitioned to the northern (49.6$\%$) and southern (50.4$\%$) management units using the values described in Appendix A of the 2021 stock assessment [@Langseth_status_2021].
 
-The target rebuilding year based on the various rebuilding strategies ranged from `r min(reb[[1]]$rebuild_quants$Ttarget)` -- `r max(reb[[2]]$rebuild_quants$Ttarget)` (Table \ref{tab:reb-options}). The probability of rebuilding by year steadily increased across the alternative SPR values with full rebuilding (reaching a probability of greater than 50$\%$) by `r max(reb[[2]]$rebuild_quants$Ttarget)` when the lowest SPR of 0.50 was applied (Table \ref{tab:prob-mat} and Figure \ref{fig:prob-fig}). Note, however, that this year is beyond the year associated with $\text{T}_\text{MAX}$. The recommended removals in 2025, the first year of rebuilding, ranged between `r min(round(reb[[1]]$acl_matrix[5,-c(1,8)],2))` -- `r max(round(reb[[2]]$acl_matrix[5,2:6],2))` mt across strategies excluding the no-harvest strategy (Table \ref{tab:acl-mat}). Zero catches were observed for the first two years under the 40-10 strategy because spawning output relative to unfished spawning output was below the 10$\%$ limit through 2026. The recommended removals slowly increased by year during the rebuilding period (Figure \ref{fig:acl-fig}). The estimated overfishing limits (OFLs) for each rebuilding alternative are given in Table \ref{tab:ofl-mat}. The change in spawning output by year relative to the spawning output target, 40$\%$ of unfished, under each of the alternatives are shown by year in Table \ref{tab:rel-ssb-mat} and Figure \ref{fig:rel-ssb-fig}. 
+The target rebuilding year based on the various rebuilding strategies ranged from `r min(reb[[1]]$rebuild_quants$Ttarget)`--`r max(reb[[2]]$rebuild_quants$Ttarget)` (Table \ref{tab:reb-options}). The probability of rebuilding by year steadily increased across the alternative SPR values with full rebuilding (reaching a probability of greater than 50$\%$) by `r max(reb[[2]]$rebuild_quants$Ttarget)` when the lowest SPR of 0.50 was applied (Table \ref{tab:prob-mat} and Figure \ref{fig:prob-fig}). Note, however, that this year is beyond the year associated with $\text{T}_\text{MAX}$. The recommended removals in 2025, the first year of rebuilding, ranged between `r min(round(reb[[1]]$acl_matrix[5,-c(1,8)],2))` -- `r max(round(reb[[2]]$acl_matrix[5,2:6],2))` mt across strategies excluding the no-harvest strategy (Table \ref{tab:acl-mat}). Zero catches were observed for the first two years under the 40-10 strategy because spawning output relative to unfished spawning output was below the 10$\%$ limit through 2026. The recommended removals slowly increased by year during the rebuilding period (Figure \ref{fig:acl-fig}). The estimated overfishing limits (OFLs) for each rebuilding alternative are given in Table \ref{tab:ofl-mat}. The change in spawning output by year relative to the spawning output target, 40$\%$ of unfished, under each of the alternatives are shown by year in Table \ref{tab:rel-ssb-mat} and Figure \ref{fig:rel-ssb-fig}. 
 <!-- The harvest rate to obtain a 50% probability of recovery by $\text{T}_\text{MAX}$ corresponds to an SPR that is lower than 0.5, which represents catch that is greater than the OFL, so is not provided in the tables.  -->

write_up/ca_rebuilder/52tables.Rmd

@@ -182,6 +182,7 @@ out2 = as.data.frame(append(out, list("SPR= .550" = extra[,3]), after = 2))
 out3 = as.data.frame(append(out2, list("SPR= .650" = extra[,5]), after = 4))
 
 #And need to divide ofls (which are actually the ABC) by the buffers (other than the SPR = 0.5 strategy, and first two years across runs)
+#Note that the OFL in 2025 differs across runs due to rounding because for SPR=0.5 just used ACL, whereas for other runs calculated the buffer. The March 2024 council meeting the SSC stated that the OFL is 1.52 (so they rounded up just a bit).
 #Cap buffers to the cat3 buffer (which is what rebuild.exe does too (sigma = 2.0))
 buffer <- PEPtools::get_buffer(2021:reb[[1]]$tmax,1,0.45)
 buffer[which(buffer[,2]<0.778),2] <- 0.778

write_up/ca_rebuilder/60appendix.Rmd

@@ -7,11 +7,5 @@ The rebuild.dat file used for the base rebuilding analysis is provided below. No
 
 \clearpage
 
-## Appendix B: Rebuilding results when using a lower value for assumed total removals in 2024 {#append_b}
-
-At its September 2023 meeting, the Council requested a value of `r round(reb_alt[[1]]$acl_matrix[4,2],2)` mt be used for assumed total removals in 2024 instead of `r round(reb[[1]]$acl_matrix[4,2],2)` mt. A second rebuilding analysis was done that was identical in all aspects to the rebuilding analysis described within the main text of this report except that the assumed 2024 removal value was set to `r round(reb_alt[[1]]$acl_matrix[4,2],2)` mt. Due to the timing of the Council's request, the tables and figures from this second rebuilding analysis are added to the report as an appendix.
-
-Rebuilding when assuming removals in 2024 were `r round(reb_alt[[1]]$acl_matrix[4,2],2)` mt resulted in $\text{T}_\text{MIN}$ and $\text{T}_\text{MAX}$ occurring one year earlier compared to assuming removals in 2024 were `r round(reb[[1]]$acl_matrix[4,2],2)` mt (Table \ref{tab:ref-points-alt}). The increase in estimated ACL in 2025 was at most `r max(round(reb_alt[[2]]$acl_matrix[5,],2) - round(reb[[2]]$acl_matrix[5,],2))` mt across alternative strategies and time to recovery was between zero and one year sooner (Table \ref{tab:reb-options-alt}). 
-