report.Rmd

---
output:
  word_document:
    fig_caption: true
    fig_height: 10
    fig_width: 10
    reference_docx: boot/data/reportTemplate.docx
    toc: true
    keep_md: false
  html_document: default
bibliography: boot/DATA.bib
nocite: '@*'
---

```{r libraries, include=FALSE}
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, lets choose 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 to get the numbering correct
table_nums("catch_table", "Estimated catch at age.")

# set figure captions in the order they appear in the report to get the numbering correct
figure_nums("retro_plot", "Retrospective of SSB, F and Recruitment (age 0).")
figure_nums("fbar_plot", "Plot of F bar (3-5) from the final assessment run.")
```



# Example Stock report

## Example stock in ICES Division 4

### Catch data

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

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

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


### Retrospective

```{r mohns}
mohns <- read.taf("output/mohns_rho.csv")
```

The mohns rho value for F is `r round(mohns[1,"Fbar(3-7)"], 3)`.  The
plot of the retrospective is plotted in `r figure_nums("retro_plot", display = "cite")`

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

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


### F at age estimate

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

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



# References

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