New index plots + chl_pp

[andybeet]

New plotting functions

• plot_benthos_index
• plot_zooplankton_index

Updates

• plot_chl_pp - nested plot_phyto_size within.
  • added an additional option to varName = "size"
  • added additional argument "EPU"
  • plots weekly baseline for year along with partial data
• updated chl_pp.r to reflect both phyto size and chl, pp
• removed phyto_size.r
• plot_aggregate_biomass bug fix (removed unneeded filter)

Other changes

• Created benthos_index.r and zooplankton_index.r data documentation files

[andybeet]

@BBeltz1 the phyto_size figure produced isn't correct. i think it is an issue with the data not the plot. Not sure exactly what is causing the problem but i think some rows are missing from the updated data set relative to what is in the ecodata::phyto_size data object.

[sgaichas]

@andybeet thank you this is a great start on the benthic and zooplankton index plots. The plots themselves look great.

I think we need to add another selection variable besides index and cog because unlike the forage index, there are multiple species groups included in these datasets. I think these are plotting only the first index of each.

benthic_index has indices for Megabenthos and Macrobenthos that need separate plots

zooplankton_index has indices for Calfin, Euph, Smallcopesoe, Lgcopeall, and Zoopvol (there should also be a Smallcopeall variable name)

So I think we need a structure more like that in plot_comdat where there is a varName argument that gets one of the names above and an plottype argument that is either index or cog

We should also include the variable name in the plot title

@BBeltz1 I think there are some variables missing in the zooplankton_index dataset because as noted when I submitted in October the google form limited me to 10 datasets; the additional ones were submitted as supplemental files

[BBeltz1]

@sgaichas Ah I see the files I missed, my mistake. I've added smallcopeALL to the dataset. Sorry for the trouble.

Just to double check Sarah, is that now everything? 6 functional groups, 4 datafiles each (fall index, fall cog, spring index, spring cog)? The dataset now has 72 variables... 6 groups x 3 variables + 3 SEs x 2 seasons. Does that sound correct?

[sgaichas]

@BBeltz1 yes I think that sounds like the correct number, thanks for checking

[andybeet]

@sgaichas @BBeltz1. i'll fix those plots.

[andybeet]

Just noticed in the catalog submission (# 122), it should be benthos_index not benthic_index. We should rename the data object, then i can update the plot functions etc

[BBeltz1]

I believe benthos_index was the originally proposed name, but there was a suggestion to switch it to benthic_index. It is now benthic_index everywhere except in the submission issues. I would propose that we leave the data object and plot function as benthic_index and change the data name in the issues to match. Unless @sgaichas has a strong preference for benthos_index.

[andybeet]

ok. i changed the indicator name to benthic_index in the submission. Also changed the name to zooplankton_index for that submission too.

EDIT: changed back to benthos_index- as agreed upon

[BBeltz1]

plotting for benthic_index, zooplankton_index and chl_pp are all working for me

[BBeltz1]

close #190