ensure that ANPP_woody_stem records show up in the variables table

[teixeirak]

@ValentineHerr , I noticed that there are no records for ANPP_woody_stem in this table, although we've definitely sent some (e.g., Piponiot study). The problem may be that the table is not up to date (#42 ) or that I'm expecting ANPP_woody_stem records to show up as part of ANPP_woody (lumping for simplicity). I the problem is the latter, could you please adjust code such that these show up as part of ANPP_woody?

[teixeirak]

AGB or Classified otherwise (OTH) would be broader categories. I think the issue is just that ForC makes a fairly fine distinction between ANPP_woody and ANPP_woody_stem that I'm dropping for the purposes of this paper. I think that at some point your code just pulls ANPP_woody and doesn't pull in ANPP_woody_stem.

[ValentineHerr]

ok I look into this more carefully

[ValentineHerr]

OK, the following variable are filtered out because the script only looks at variables listed in this file. Can you tick the variables that should not be dropped and should be lumped into another?

• [ ] NEE
• [ ] NEE_cum
• [ ] NEP
• [ ] GPP
• [ ] GPP_cum
• [ ] TBCF
• [ ] NPP_1
• [ ] NPP_2
• [ ] NPP_3
• [ ] NPP_4
• [ ] NPP_5
• [ ] NPP_0
• [ ] NPP_understory
• [ ] ANPP_1
• [ ] ANPP_2
• [ ] ANPP_0
• [x] ANPP_woody_stem
• [x] ANPP_woody_branch
• [ ] ANPP_foliage
• [x] ANPP_litterfall_1
• [x] ANPP_litterfall_2
• [ ] ANPP_litterfall_0
• [ ] ANPP_repro
• [ ] ANPP_folivory
• [x] BNPP_root
• [ ] R_eco
• [ ] R_eco_cum
• [ ] R_auto
• [ ] R_auto_ag
• [ ] R_auto_wood
• [ ] R_auto_foliage
• [ ] R_auto_root
• [ ] R_soil
• [ ] R_het_ag
• [ ] R_het
• [ ] delta.total.ecosystem
• [ ] delta.total.ecosystem_2
• [ ] delta.organic.layer
• [ ] total.ecosystem
• [ ] total.ecosystem_2
• [ ] biomass_ag_understory
• [ ] organic.layer
• [ ] stand.density
• [ ] LAI
• [ ] leaf_pC
• [ ] leaf2N
• [ ] leaf_pN
• [ ] foliage_pN
• [ ] leaf_pCa
• [ ] leaf_pK
• [ ] leaf_pMg
• [ ] leaf_pP
• [ ] stem_pC
• [ ] stem_pN
• [ ] root_pN
• [ ] root_pC
• [ ] soil_pC
• [ ] soil2N
• [ ] N.mineralization
• [ ] max.diameter
• [ ] min.diameter
• [ ] max.diameter_branch
• [ ] min.diameter_branch
• [ ] max.diameter_twig
• [ ] max.diameter_root
• [ ] min.diameter_root
• [ ] min.diameter_liana
• [ ] min.height
• [ ] max.height
• [ ] min.length
• [ ] min.depth
• [ ] u.star
• [ ] stem.level
• [ ] include.recruitment

[ValentineHerr]

For the variables that needs their own rows, if you add them in that C_variables_order_template.csv file, they will be pulled in the summary table.

[teixeirak]

I see NPP_woody in this list, but it's also in this table. Ditto for ANPP_woody.

[teixeirak]

ANPP_woody_branch

Not sure what to do about this one. IPCC wants it, but it's a minor variable and I'd prefer not to bog down the figure and table with it. I'll come back to this.

[ValentineHerr]

I see NPP_woody in this list, but it's also in this table. Ditto for ANPP_woody.

oops.. sorry, I'll see what happened there.

[teixeirak]

I see NPP_woody in this list, but it's also in this table. Ditto for ANPP_woody.

Actually, I think that's a list of all variables.

Those of interest to IPCC are in the provide.to.IPCC field of this file.

There's some discrepancy between the ones that IPCC wants and the ones I wanted to show in the figure & table. I need to think about that.

[teixeirak]

What would be helpful is to get a list of the variables not in this table but flagged in the provide.to.IPCC field of this file.

[teixeirak]

I guess we need to either list them all or create an "other variables" category.

[ValentineHerr]

FYI, edited the list. It now only shows the ones that are not in the C_variables_order_template.csv file.

We look into your other comments now.

[ValentineHerr]

What would be helpful is to get a list of the variables not in this table but flagged in the provide.to.IPCC field of this file.

Here it is

• [ ] ANPP_woody_stem
• [ ] ANPP_woody_branch
• [ ] ANPP_litterfall_1
• [ ] ANPP_litterfall_2
• [ ] BNPP_root
• [ ] delta.total.ecosystem_2
• [ ] biomass_ag_understory

[teixeirak]

I edited your list to remove covariates.

[ValentineHerr]

I guess we need to either list them all or create an "other variables" category.

The main concern is space in the C_variable_mapping.png diagram?

[teixeirak]

Here's my list of what to do with each (I'll edit this gradually):

• [x] ANPP_woody_stem - change variable mapping figure to read ANPP_woody(_stem) (KAT), add as new row after ANPP_woody in table
• [x] ANPP_woody_branch (243 records in ForC) - add footnote on figure (KAT), add as new row after ANPP_woody_stem in table
• [x] ANPP_litterfall_1 - edit names on mapping figure under both foliage and litter (KAT), include in table with NPP_litter, renaming row as "ANPP_litter / NPP_litter"
• [x] ANPP_litterfall_2 - same as above
• [x] BNPP_root - add to table as new row (above BNPP_root_fine)
• [x] delta.total.ecosystem_2 (0 records in ForC)- add footnote on figure (KAT), in table (before soil C) add new header row "Total Ecosystem C", and place this underneath (after total.ecosystem_2).
• [x] total.ecosystem_2 (64 records in ForC)- add footnote on figure (KAT), in table (before soil C) add new header row "Total Ecosystem C", and place this underneath (before delta.total.ecosystem_2).
• [x] biomass_ag_understory - add footnote on figure (KAT), include with biomass_ag (no edit to variable name in table)
• [x] stem_pC (9 records in ForC) - add footnote on figure (KAT), add as new row at end of "aboveground biomass" category

[teixeirak]

@ValentineHerr , I think the above list is good now.

[teixeirak]

Replicating the list above so that I can check off my edits:

Here's my list of what to do with each (I'll edit this gradually):

• [x] ANPP_woody_stem - change variable mapping figure to read ANPP_woody(_stem) (KAT), add as new row after ANPP_woody in table
• [x] ANPP_woody_branch (243 records in ForC) - add footnote on figure (KAT), add as new row after ANPP_woody_stem in table
• [x] ANPP_litterfall_1 - edit names on mapping figure under both foliage and litter (KAT), include in table with NPP_litter, renaming row as "ANPP_litter / NPP_litter"
• [x] ANPP_litterfall_2 - same as above
• [x] BNPP_root - add to table as new row (above BNPP_root_fine)
• [x] delta.total.ecosystem_2 (0 records in ForC)- add footnote on figure (KAT), in table (before soil C) add new header row "Total Ecosystem C", and place this underneath (after total.ecosystem_2).
• [x] total.ecosystem_2 (64 records in ForC)- add footnote on figure (KAT), in table (before soil C) add new header row "Total Ecosystem C", and place this underneath (before delta.total.ecosystem_2).
• [x] biomass_ag_understory - add footnote on figure (KAT), include with biomass_ag (no edit to variable name in table)
• [x] stem_pC (9 records in ForC) - add footnote on figure (KAT), add as new row at end of "aboveground biomass" category

[ValentineHerr]

let me know when you've pushed your edits

[teixeirak]

For the variables that needs their own rows, if you add them in that C_variables_order_template.csv file, they will be pulled in the summary table.

Oops, I missed this. Will do it now.

[teixeirak]

when multiple variables should be combined in the same row, should I separate with "/"? It looks like that's what we did for SOC/ SOM.

[ValentineHerr]

when multiple variables should be combined in the same row, should I separate with "/"? It looks like that's what we did for SOC/ SOM.

Hmmm... I think in that case it is just showing the variable "soil" as SOM/SOC, it is not pulling any variables together.

[ValentineHerr]

For now add a row but repeat the value in the third column (variable).

[teixeirak]

Oh, so variable is what's displayed? (I'll need to adjust what I've been doing.)

[ValentineHerr]

Oh, so variable is what's displayed? (I'll need to adjust what I've been doing.) yes. I use that table to have an easy way to order he variables in the way you wanted, and also to display prettier names