The distribution by box plots show numbers but I think it would also be useful to see the density per m3. Is it possible to add this as an option?

Also, I think the interactive plot would benefit from showing density per m2 in a box and skip the layers.

Create a trellis plot where you select each box and see which species are present in what layers in the box.

Scale for the animated plots jumps too much. It would be useful to create a scale that is static.

I wanted to suggest a diagnostic plot that would be extremely useful in the calibration phase.
I am not so sure what would be the best way to implement it, but the basic idea is to visualize whether predator distribution (by box and layer) matches its preys (defined in the diet matrix of the biom.prm). I find that trophic interaction is one of the most critical but also tricky bit in Atlantis.
Maybe a way to do it could be to add in the spatial plots a prey-pred overlap, for which by selecting a predator, you can see in which boxes and layers preys are available.
Please let me know what you think.

Create a biomass or biomass density (biomass/volume of layer) for each box by trophic level. How do define trophic level though ...

For Hake, should have two ages classes but their order in _mat_age file differed from their order in the ncdf4 file. Therefore, they were getting assigned the wrong age classes.

Updating to ggplot2 version 2 (the version on CRAN) breaks the UI for the Age Disaggregated tab (namely the proportion of each age class plot, upper right).

The YOY biomass plot looks very strange. Either it's something wrong with Atlantis code or my code.

Also I wanted to suggest converting the units of structural and reserve
weights (mgN) in the age disaggregated plot to g of wet weight (gWW):
gWW = (mgN * 5.7 * 20)/1000

If the biol.prm file contains another number (ie, a recommended value, or a previously used value), the code for mat_age joins them together, so you can get a large age at maturity. I edited this (rather clumsily, but it works) to take just the first number
mat_age <- grep("_age_mat", biolprm, value = T)
species_ids <- str_split_fixed(mat_age, "_age_mat", n = 2)[,1]

juvenile_age <- as.numeric(gsub("[^\d]+", "", mat_age, perl=TRUE))[which(species_ids %in% vert_names)]

#test how many numbers there are. Sometimes there is an example value as well as the actual value,
#in which case we only want the first one
get_first_number<-function(x){
yy<-gsub("([^\d])","#",x,perl=TRUE)
yyy<-unlist(str_split(yy,"#"))
xPos<-grep("[^\d]",yyy)[1]
thisNum<-as.numeric(yyy[xPos])
}
temp<-lapply(mat_age,FUN=get_first_number)
juvenile_age<-as.numeric(unlist(temp))

Add an argument to make fishing output optional.

Christopher:

Hi, I've tried to install vat but run into an error with dependency on netcdf4. I wanted to see if you had any suggestions.
If I am running R in a 64-bit Windows 7 system. If I run 32-bit R,install netcdf4 for 32bit and try to install vat I get an error that netcdf is not installed on arch x64. Conversely if I run 64-bit R,install netcdf4 for 64bit and try to install vat I get an error that netcdf is not installed on arch xi386.

Thanks!

Hem Nalini Morzaria

install_github(repo = "cddesja/vat", )
Downloading github repo cddesja/vat@master
Installing vat
"C:/Users/HemNalini.MorzariaLu/Documents/R/R-3.1.2/bin/i386/R" --vanilla CMD INSTALL
"C:/Users/HemNalini.MorzariaLu/AppData/Local/Temp/1/RtmpMPyZWR/devtools397c5f011eab/cddesja-vat-5ee7bff"
--library="C:/Users/HemNalini.MorzariaLu/Documents/R/win-library/3.1" --install-tests

• installing source package 'vat' ...
  ** R
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  *** arch - i386
  *** arch - x64
  Error : package 'ncdf4' is not installed for 'arch = x64'
  Error: loading failed
  Execution halted
  ERROR: loading failed for 'x64'
• removing 'C:/Users/HemNalini.MorzariaLu/Documents/R/win-library/3.1/vat'
  Error: Command failed (1)

When I ran it, create_vadt fell over unless I made everything 'gather' was to be used on a data.frame

Create biomass plots over time collapsed over age class in one page using a facet grid. Do this separate for vertebrates and invertebrates.

Remove the final plots in Age Disaggregated tab as it's redundant with other plots in this tab.

Hi,

I've tried to run this package with the test files SETas , provided with the Atlantis code.
However, I keep on receiving this error after entering the necessary input files into the create_vadt() function;

Error: Each variable must be named.
Problem variables: 34

What am I doing wrong?