pull all catch from catch.nc file

[andybeet]

atlantistools::load_nc does not read in all of the species catch. Probably because species names are formatted differently..

eg.

library(ncdf4)
x.nc = nc_open(here::here('Atlantis_Runs','master_2_2_0','neus_outputCATCH.nc'))
varname = names(x.nc$var)
vn1 <- grep('SCA',varname,value = T)
vn2 <- grep('Smooth',varname,value = T)
nc_close(x.nc)

Results in

[1] "SCA_Catch_FC1"   "SCA_Discard_FC1"

and

 [1] "Smooth_Dogfish1_Catch"    "Smooth_Dogfish2_Catch"    "Smooth_Dogfish3_Catch"    "Smooth_Dogfish4_Catch"   
 [5] "Smooth_Dogfish5_Catch"    "Smooth_Dogfish6_Catch"    "Smooth_Dogfish7_Catch"    "Smooth_Dogfish8_Catch"   
 [9] "Smooth_Dogfish1_Discards" "Smooth_Dogfish2_Discards" "Smooth_Dogfish3_Discards" "Smooth_Dogfish4_Discards"
[13] "Smooth_Dogfish5_Discards" "Smooth_Dogfish6_Discards" "Smooth_Dogfish7_Discards" "Smooth_Dogfish8_Discards"