gf-smms-techreport/98-appendix-body.rmd at main · pbs-assess/gf-smms-techreport · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

\begin{landscapepage}

\chapter{Timeline of SMMS survey changes}\label{app:change-table} % use chapter so that it gets turned into \section in latex


```{r change-table, echo=FALSE, eval=TRUE}
mssm_survey_changes <- readr::read_csv(here::here('data', 'mssm-survey-changes.csv')) |>
  mutate(across(everything(), ~tidyr::replace_na(.x, ""))) |>
   mutate(across(where(is.character), ~kableExtra::linebreak(.x, linebreaker = "::")))

csasdown::csas_table(mssm_survey_changes, caption = "Summary of changes to the Small-mesh Multi-species bottom trawl survey (SMMS). These changes are compiled from Rutherford et al. In prep.", format = "latex", escape = FALSE) |>
  # kableExtra::row_spec(0, extra_latex_after = "\\addlinespace[5pt]") |>  # Add spacing before the first row
  kableExtra::row_spec(1:nrow(mssm_survey_changes), extra_latex_after = "\\addlinespace[5pt]") |>
  kableExtra::column_spec(1, width = "1.7cm") |>
  kableExtra::column_spec(2, width = "6cm") |>
  kableExtra::column_spec(3, width = "7cm") |>
  kableExtra::column_spec(4, width = "7.5cm")

# For producing table in word
  # flextable::flextable(mssm_survey_changes) |>
  # flextable::set_caption(caption = "Summary of changes to the Small-mesh Multi-species bottom trawl survey (SMMS). These changes are compiled from Rutherford et al. In prep.") |>
  # #flextable::set_table_properties(layout = "autofit") |>
  # flextable::width(width = c(1.5, 4.3, 9.3), j = 1:3)

```
\end{landscapepage}

\clearpage

# Size distributions over time {#app:size-time}

Comparison of fish lengths sampled in the Small-mesh Multi-species (SMMS)  and the Synoptic West Coast Vancouver Island (SYN WCVI) bottom trawl surveys over time. Species are ordered by decreasing median size differences observed between the two surveys (Figure \@ref(fig:size-dist-time)).

(ref:size-time0-cap) Same as Figure \@ref(fig:size-dist-time) for additional species.

(ref:size-time1-cap) Same as Figure \@ref(fig:size-dist-time) for additional species.

(ref:size-time2-cap) Same as Figure \@ref(fig:size-dist-time) for additional species.

(ref:size-time3-cap) Same as Figure \@ref(fig:size-dist-time) for additional species.


```{r size-time0, fig.cap="(ref:size-time0-cap)"}

knitr::include_graphics(here::here("figure/size-time-0.png"), dpi = NA)

```

```{r size-time1, fig.cap="(ref:size-time1-cap)"}

knitr::include_graphics(here::here("figure/size-time-1.png"), dpi = NA)

```

```{r size-time2, fig.cap="(ref:size-time2-cap)"}

knitr::include_graphics(here::here("figure/size-time-2.png"), dpi = NA)

```

```{r size-time3, fig.cap="(ref:size-time2-cap)"}

knitr::include_graphics(here::here("figure/size-time-3.png"), dpi = NA)

```