In NOAA-EDAB/ms-keyrun: All information for keyrun review

knitr::opts_chunk$set(echo = TRUE)

catHeader <- function(text = "", level = 3) {
  cat(paste0("\n\n", 
               paste(rep("#", level), collapse = ""), 
               " ", text, "\n"))
}

The length based multispecies model (Hydra) requires annual indices of biomass and abundance by species size class. The NEFSC spring and fall bottom trawl surveys collect the information required to obtain estimates of these indices

Each tow/haul during the bottom trawl survey collects the total weight of each fish species caught. A sample of the haul is then taken and each fish in this sample is identified, lengthed (to the nearest cm) and weighed.

The R package survdat is used to read in the survey data and provide estimates of swept area biomass and abundance on the Georges Bank footprint. The survey strata that define Georges Bank are 1090, 1130:1210, 1230, 1250, 3460, 3480, 3490, 3520:3550.

``` {r, echo = T} source(here::here("data-raw/R/create_real_survey_lennumcomp.R")) suppressMessages(out <- create_real_survey_lennumcomp(convertKGtoMT=T))

<!-- ## Spring Biomass: length-frequency plots {.tabset} -->

<!-- ```r -->
<!-- for(i in seq_along(out$plistBS)){ -->
<!--     tmp <- out$plistBS[[i]] -->
<!--     # As you want to use tabset level here has to be lower than  -->
<!--     # parent level (ie, parent is 2, so here you have to use 3) -->
<!--     catHeader(tmp[[2]], 3) -->
<!--     lapply(tmp[1], print) -->
<!-- } -->
<!-- ``` -->


<!-- ## Fall Biomass: length-frequency plots {.tabset} -->

<!-- ```r -->
<!-- for(i in seq_along(out$plistBF)){ -->
<!--     tmp <- out$plistBF[[i]] -->
<!--     # As you want to use tabset level here has to be lower than -->
<!--     # parent level (ie, parent is 2, so here you have to use 3) -->
<!--     catHeader(tmp[[2]], 3) -->
<!--     lapply(tmp[1], print) -->
<!-- } -->
<!-- ``` -->

## Spring Abundance: length-frequency plots {.tabset}

```r
for(i in seq_along(out$plistAS)){
    tmp <- out$plistAS[[i]]
    # As you want to use tabset level here has to be lower than 
    # parent level (ie, parent is 2, so here you have to use 3)
    catHeader(tmp[[2]], 3)
    lapply(tmp[1], print)
}

Fall Abundance: length-frequency plots {.tabset}

for(i in seq_along(out$plistAF)){
    tmp <- out$plistAF[[i]]
    # As you want to use tabset level here has to be lower than
    # parent level (ie, parent is 2, so here you have to use 3)
    catHeader(tmp[[2]], 3)
    lapply(tmp[1], print)
}