testing load_detailed_diet from atlantisom — est_trophic

Need to process detailed diet data frirst linux command line

Usage

est_trophic_level(
  param.dir =
    "C:/Users/andrew.beet/Documents/myWork/githubRepos/neus-atlantis/currentVersion",
  atl.dir = here::here("other/dev_3a75e57d1"),
  fgs = "neus_groups.csv",
  detDietfile = "DetDiet2.gz",
  plottl = F
)

Arguments

param.dir: Character String. Path to Parameter directory
atl.dir: Character String. Path to output directory
fgs: Character String. Name of groups.csv file
detDietfile: Character String. Name of processed zipped detailed diet file
plottl: Boolean. Plot the Trophic level to window. Default = F

Value

list

trophiclevel: dataframe. Species, year, trophic level
figuretl: ggplot2 object. trophic level bar plot by species

zip up file

gzip -k neus_outputDetailedDietCheck.txt then remove zeros and save ans another zip zcat neus_outputDetailedDietCheck.txt.gz | awk 'NR > 1s=0; for (i=6;i<=NF;i++) s+=$i; if (s!=0)print' | gzip > DetDiet.gz strip headers from original file zcat neus_outputDetailedDietCheck.txt.gz | head -n1 | gzip > DetDietHead.gz concatenate them cat DetDietHead.gz DetDiet.gz > DetDiet2.gz