report.Rmd

---
output:
  word_document:
    fig_caption: true
    fig_height: 10
    fig_width: 10
    reference_docx: bootstrap/data/reportTemplate.docx
    toc: true
    keep_md: false
---

```{r libraries, include=FALSE}
taf.library(captioner)
library(knitr)
library(pander)
```

```{r chunk_setup, include=FALSE}
# CHUNK SETUPS #################################################################
knitr::opts_chunk$set(echo = FALSE, warning = FALSE,
                      message=FALSE, results = 'asis')
```

```{r pander_settings, include = FALSE}
# PANDER OPTIONS ##############################################################
panderOptions('table.split.table', Inf)
panderOptions('keep.trailing.zeros', TRUE)
panderOptions('table.alignment.default', "center")
```

```{r caption_counters, include=FALSE}
table_nums <- captioner("Table", level = 3)
figure_nums <- captioner("Figure", level = 3)

# set levels, sandeel 6 is section 9.6
tab_env <- environment(table_nums)
fig_env <- environment(figure_nums)
tab_env$OBJECTS$number[[1]] <- list(9, 6, 1)
fig_env$OBJECTS$number[[1]] <- list(9, 6, 1)

# set table captions in the order they appear in the report
table_nums("catch_table", "Sandeel. Total catch (tonnes) for the first and second half of the year as estimated by ICES")

# set figure captions in the order they appear in the report
figure_nums("catch_plot", "Sandeel. Total catch (tonnes) by year as estimated by ICES.")

figure_nums("catch_plot2", "Sandeel. Total catch (tonnes) by year for the first and second half of the year as estimated by ICES.")
```

# Sandeel in Division 3.a and Subarea 4

## Sandeel in SA 6

### Catch data

Total catch weight by year for SA 6 is given in `r table_nums("catch_table", display = "cite")`, and plotted in `r figure_nums("catch_plot", display = "cite")` and `r figure_nums("catch_plot2", display = "cite")`


```{r catch_table}
catch_table <- read.taf("report/summary_catch.csv")

# set caption
set.caption(table_nums("catch_table"))

# Output table
pander(style_table1(catch_table), missing = "-")
```


```{r catch_plot, fig.cap = cap_in}
# Figure Caption
cap_in <- figure_nums("catch_plot")

# Output figure
include_graphics("report/summary_catch.png")
```

```{r catch_plot2, fig.cap = cap_in}
# Figure Caption
cap_in <- figure_nums("catch_plot2")

# Output figure
include_graphics("report/catches_by_halfyear_bar.png")
```