In jae0/snowcrab: Snow crab assessment suite for aegis* and associated projects.

  require(knitr)
  knitr::opts_chunk$set(
    root.dir = data_root,
    echo = FALSE,
    out.width="6.2in",
#     dev.args = list(type = "cairo"),
    fig.retina = 2,
    dpi=192
  )

  # inits and data loading (front load all required data)

  require(aegis)

  year.assessment = params$year.assessment
  year_previous = year.assessment - 1
  p = bio.snowcrab::load.environment( year.assessment=year.assessment )
  SCD = project.datadirectory("bio.snowcrab")
  media_loc = params$media_loc

  # fishery_model_results = file.path( "/home", "jae", "projects", "dynamical_model", "snowcrab", "outputs" )
  fishery_model_results = file.path( SCD, "fishery_model" )

  sn_env = snowcrab_load_key_results_to_memory( year.assessment, debugging=params$debugging, loc_dde=params$loc_dde, return_as_list=TRUE  ) 

  attach(sn_env)

  # predator diet data
  diet_data_dir = file.path( SCD, "data", "diets" )
  require(data.table) # for speed
  require(lubridate)
  require(stringr) 
  require(gt)  # table formatting
  library(janitor)
  require(ggplot2)
  require(aegis) # map-related 
  require(bio.taxonomy)  # handle species codes

  # assimilate the CSV data tables:
  # diet = get_feeding_data( diet_data_dir, redo=TRUE )  # if there is a data update
  diet = get_feeding_data( diet_data_dir, redo=FALSE )
  tx = taxa_to_code("snow crab")  
  # matching codes are 
  #  spec    tsn                  tx                   vern tx_index
  #1  528 172379        BENTHODESMUS           BENTHODESMUS     1659
  #2 2522  98427        CHIONOECETES SPIDER QUEEN SNOW UNID      728
  #3 2526  98428 CHIONOECETES OPILIO        SNOW CRAB QUEEN      729
  # 2 and 3 are correct

  snowcrab_predators = diet[ preyspeccd %in% c(2522, 2526), ]  # n=159 oservations out of a total of 58287 observations in db (=0.28% of all data)
  snowcrab_predators$Species = code_to_taxa(snowcrab_predators$spec)$vern
  snowcrab_predators$Predator = factor(snowcrab_predators$Species)

  counts = snowcrab_predators[ , .(Frequency=.N), by=.(Species)]
  setorderv(counts, "Frequency", order=-1)

  # species composition
  psp = speciescomposition_parameters( yrs=p$yrs, runlabel="1999_present" )
  pca = speciescomposition_db( DS="pca", p=psp )  

  pcadata = as.data.frame( pca$loadings )
  pcadata$vern = stringr::str_to_title( taxonomy.recode( from="spec", to="taxa", tolookup=rownames( pcadata ) )$vern )

  # bycatch summaries
  o_cfaall = observer.db( DS="bycatch_summary", p=p,  yrs=p$yrs, region="cfaall" )
  o_cfanorth = observer.db( DS="bycatch_summary", p=p,  yrs=p$yrs, region="cfanorth" )   
  o_cfasouth = observer.db( DS="bycatch_summary", p=p,  yrs=p$yrs, region="cfasouth" )   
  o_cfa4x = observer.db( DS="bycatch_summary", p=p,  yrs=p$yrs, region="cfa4x" )