longtable issue

Started changing lontable = FALSE, messed up on .tex files though
pfmc-assessments · Mar 9, 2024 · c420a3d · c420a3d
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diff --git a/documents/_main.tex b/documents/_main.tex
diff --git a/documents/nca/00a.md b/documents/nca/00a.md
diff --git a/documents/nca/00bibliography.Rmd b/documents/nca/00bibliography.Rmd
@@ -0,0 +1,6 @@
+---
+bibliography:
+  - sa4ss.bib
+  - wcassess.bib
+  - pfmcassess.bib
+---
diff --git a/documents/nca/52tables.Rmd b/documents/nca/52tables.Rmd
@@ -23,7 +23,7 @@ col_names = c("Year", "Commercial Dead", "Commercial Live", "CPFV", "PR", "Total
 
 table_format(x = out,
              caption = "Removals (mt) by fleet and the summed total landings (mt).",
-             label = "allcatches",
+             longtable = FALSE, label = "allcatches",
              digits = 1,
              align = 'l',
              col_names = col_names)
@@ -149,7 +149,7 @@ col_names <- c("Year", "Source", "Number of Ages")
 
 sa4ss::table_format(x = tab,
              caption = "Available age data by year and source used in the growth fleets.",
-             label = "growth-age-samps",
+             longtable = FALSE, label = "growth-age-samps",
              align = 'l',
              col_names = col_names,
              custom_width = TRUE,
@@ -172,7 +172,7 @@ col_names <- c("Year", "UCSC Raw Count", "UCSC Filtered Count", "UCSB Raw Count"
 
 table_format(x = tab,
              caption = "All and filtered observations by year and sampling institution for PISCO.",
-             label = "pisco-data",
+             longtable = FALSE, label = "pisco-data",
              align = 'l',
              col_names = col_names)
 ```
@@ -275,7 +275,7 @@ col_names <- c("Fleet", "Data Type", "Francis", "MI", "Dirichlet")
 
 sa4ss::table_format(x = tab,
              caption = "Suggested data weights for each data weighting methodology by fleet and data type.",
-             label = "dw",
+             longtable = FALSE, label = "dw",
              align = 'l',
              digits = 2,
              col_names = col_names) 

diff --git a/documents/nca/62appendix_crfs_onboard.Rmd b/documents/nca/62appendix_crfs_onboard.Rmd
@@ -39,8 +39,7 @@ or the history of regulation changes section for details.
 The filters also included removal of the number of observed anglers and time fished at the tail 
 ends of the distributions and removal of drifts occurring in depths outside copper rockfish's range 
 (Table \@ref(tab:onboard-filter) and Figure \@ref(fig:onboard-depths)). 
-We retained 17,458 drifts for index
- standardization, and 3,303 of those drifts encountered copper rockfish 
+We retained 17,458 drifts for index  standardization, and 3,303 of those drifts encountered copper rockfish 
 Table \@ref(tab:onboard-percentpos). 
 
 We modeled catch per angler minutes fished (CPUE) by fishing drift. 
@@ -65,17 +64,16 @@ known area of rocky substrate to areas in southern California that lack substrat
 expansion of the estimated rocky substrate assumes that the proportions of rocky substrate within 
 and outside state waters are similar.  Copper rockfish are a nearshore species and the majority of 
 observed encounters were within state waters (Table \@ref(tab:onboard-waterarea)).
-This is, of course, an estimation of the amount of rocky substrate, and represents the best available data. The calculations can be found in the online supplementary material. Starting in 2017, depth restrictions eased in districts 
+This is, of course, an estimation of the amount of rocky substrate, and represents the best available data. 
+The calculations can be found in the online supplementary material. Starting in 2017, depth restrictions eased in districts 
 north of Point Conception and the recreational fleet targeted these depths 
 (Figure \@ref(fig:onboard-depths)). The deeper waters (40-50 fm) are 
 outside of the mapped hard bottom habitat, but could be assigned to the larger 
 areas considered as a factor in the index.
 
 
-The covariates explored for model selection included year and four categorical region levels (CRFS Districts 3-6), a categorical variable for month, and continuous depth and depth-squared. Trends in the average CPUE by region were similar in the filtered data set (Figure \@ref(fig:onboard-regioncpue)). A year and region interaction 
-was included after visualizing the trends in average CPUE over time, but was not significant. The full model was selected by AICc and 
-included year, depth, depth squared and region
-(Table \@ref(tab:onboard-model_selection)). 
+The covariates explored for model selection included year and four categorical region levels (CRFS Districts 3-6), a categorical variable for month, and continuous depth and depth-squared. Trends in the average CPUE by region were similar in the filtered data set (Figure \@ref(fig:onboard-regioncpue)). A year and region interaction was included after visualizing the trends in average CPUE over time, but was not significant. The full model was selected by AICc and 
+included year, depth, depth squared and region (Table \@ref(tab:onboard-model_selection)). 
 
 Indices were fit via MLE from the sdmTMB package in R. The Q-Q plot for the negative binomial model indicated a poor fit to the data, which as not surprising given the low percent of observed drifts encountering copper rockfish. A delta-Lognormal 
 was selected over a delta-gamma by a delta AIC of 487.  The Q-Q plot indicated a much 
@@ -85,19 +83,19 @@ and Figure \@ref(fig:onboard-index)).
 
 
 ```{r, results = 'asis'}
-ind <- read.csv(file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",
-                    "keep_discard_prop.csv")) %>%
+library(dplyr)
+ind <- read.csv(file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004", "keep_discard_prop.csv")) %>%
 mutate(Proportion.discarded = round(Proportion.discarded, 3)) %>%
 mutate(Proportion.discarded = scales::percent(Proportion.discarded))
 col_names = c("Year", "Number Kept", "Number Discarded", "Proprtion Discarded")
 
 sa4ss::table_format(x = ind,
              caption = "Number of observed copper rockfish retained and discarded by year.",
-             label = "onboard-keepdiscard",
+             longtable = FALSE, label = "onboard-keepdiscard",
              col_names = col_names)                         
 ```
 
-\newpage
+
 
 ```{r, results = 'asis'}
 ind <- read.csv(file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north",
@@ -108,12 +106,12 @@ col_names = c("District", "Inside State Waters", "Outside State Waters","Percent
 
 sa4ss::table_format(x = ind,
              caption = "Number of observed drifts inside and outside of state waters by district, summed across years.",
-             label = "onboard-waterarea",
+             longtable = FALSE, label = "onboard-waterarea",
             col_names = col_names)                         
 ```
 
 
-\newpage
+
 
 ```{r, results = 'asis'}
 ind <- read.csv(file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north",
@@ -123,41 +121,23 @@ col_names = c("Year", "Samples with Target", "Samples without Target", "Total Sa
 
 sa4ss::table_format(x = ind,
              caption = "Number of samples with and without copper rockfish.",
-             label = "onboard-percentpos")#,
-        #     col_names = col_names)                         
-```
-
-\newpage
-
-```{r, results = 'asis'}
-#ind <- read.csv(file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north",
-#                    "model_selection.csv"))
-#col_names = c("Filter",	"Description",	"Number of Samples", "Positive Samples")
-
-#sa4ss::table_format(x = ind,
-#             caption = "Data filtering steps for the onboard CPFV survey.",
-#             label = "onboard-filter",
-#             col_names = col_names)                         
+             longtable = FALSE, label = "onboard-percentpos")
 ```
 
 
-\newpage
-
 ```{r, results = 'asis'}
-
 ind <- read.csv(file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",
                    "deltalogn", "index_forSS.csv"))
 ind <- ind[, c(1,4,5)]
 col_names = c("Year", "Estimate", "logSE")
 
 sa4ss::table_format(x = ind,
              caption = "Estimated relative index of abundance for the onboard CPFV survey.",
-             label = "onboard-index",
+             longtable = FALSE, label = "onboard-index",
              digits  = 4,
              col_names = col_names)                         
 ```
 
-\newpage
 
 ```{r, results = 'asis'}
 ind <- read.csv(file.path(data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",
@@ -168,7 +148,7 @@ col_names = c("Filter",	"Description",	"Number of Samples", "Positive Samples")
 sa4ss::table_format(
         x = ind,
         caption = "Data filtering steps for the onboard CPFV survey.",
-        label = "onboard-filter",
+        longtable = FALSE, label = "onboard-filter",
         col_names = col_names,
         landscape = TRUE,
         custom_width = TRUE,
@@ -177,58 +157,40 @@ sa4ss::table_format(
         width = c("8cm"))                        
 ```
 
-\newpage
 
-```{r, results = 'asis'}
-ind <- read.csv(file.path(
-  data_dir, "rec_indices", "crfs_cpfv_onboard", "north", "start2004",  "model_selection.csv"
-))
-col_names <- c("Intercept",	"Depth", "Depth-squared",	"Month", "Region", "Year", "DF",	"AICc",	"Delta AICc")
-
-#sa4ss::table_format(
-#  x = ind,
-#  caption = "Model selection for the onboard CRFS CPFV survey.",
-#  label = "onboard-model_selection",
-#  digits = 2,
-#  font_size = 8,
-#  col_names = col_names
-#)
-```
 
-\newpage
 ```{r, results = 'asis'}
 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.",
+alt_caption = "Index for the CPFV survey indicating a flat index until 2016 when the relative index indreases",
 label = 'onboard-index')
 ```
 
-\newpage
+
 
 ```{r, results = 'asis'}
 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.",
+alt_caption = "The q q plot shows a decent fit to the data",
 label = 'onboard-qq')
 ```
 
-\newpage
+
 
 
 ```{r, results = 'asis'}
 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.",
+alt_caption = "Average catch per unit effort by district showing that the trends across district are similar",
 label = 'onboard-regioncpue')
 ```
 
-\newpage
 
 ```{r, results = 'asis'}
 sa4ss::add_figure(
@@ -239,16 +201,14 @@ alt_caption = "Distribution of depths showing an increase in the mean as you mov
 label = 'onboard-depths')
 ```
 
-\newpage
+
 
 
 ```{r, results = 'asis'}
 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.",
+alt_caption = "Number of drifts with copper rockfish by depth indicating copper rockfish are mostly found shallower than 300 feet",
 label = 'onboard-depths2')
 ```
-
-\newpage