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Script to calc site level mean SOC and standard dev #72
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One helpful resource I'd still like to see is a table from SoDaH that replicates Table C1 from this paper with data from all the sites (or at least NEON, LTER, and NutNet sites). Below are some suggestions that may make this easier:
From there we'd have to think about where we want to go, but I can imagine this kind of summary table will be useful for a variety of questions & applications. |
@piersond is this something you think you're able to think about? |
@wwieder I have some time this week to start outlining a script for pulling the site means. |
I've uploaded a start to the script on GitHub, here. For now, it's a straightforward group and summarize, and the script only dives into the process of pulling together the soil C data. When we get the soil C summary to work right, I expect we can find points along the way to revise and pull MAP, MAT, etc. Script pulls the SoDaH database from the EDI script in the parent folder and all looks good so far. Questions:
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let's go ahead and lyr_soc to get more data for now. Ultimately, we
may need to use the stock data for particular applications, but working
through some of these issues with a bigger dataset seem useful.
Re. vertically resolved data:
- I think we'll want to sum over depth for individual profiles and then try
to average across profiles (as opposed to averaging across depths and
then summing the mean).
- I'd also expect we want to set an arbitrary maximum depth (e.g. 10 or 20
cm) and mask out data below that?
- Another alternative would be to just take the top measurement in each
profile, and record the bottom depth that's being recorded?
- In short, we may want to evaluate several options about how to do this...
…On Mon, Jul 13, 2020 at 7:27 PM Derek Pierson ***@***.***> wrote:
I've uploaded a start to the script on GitHub, here
<https://github.com/lter/lterwg-som/tree/main/data-aggregation/Summary%20tbl>
.
For now, it's a straightforward group and summarize, and the script only
dives into the process of pulling together the soil C data. When we get the
soil C summary to work right, I expect we can find points along the way to
revise and pull MAP, MAT, etc.
Script pulls the SoDaH database from the EDI script in the parent folder
and all looks good so far.
Questions:
1.
@wwieder <https://github.com/wwieder> The example table reports C
stocks, so I'm assuming we're confined to using lyr_soc_stock_calc? Is
lyr_soc relevant to the table without bulk density? So much more data in
lyr_soc...thoughts?
2.
@srearl <https://github.com/srearl> Any ideas on a good way to sum
soil C over depth increments? The curve ball is that sometimes the depth
increments have gaps. So, I'm thinking we'll have to pass the data one
sample location at a time through a function that can both find and
extrapolate over the depth gaps, then sum the analyte (e.g. soil C) by
depth increment to a specified target depth. I'm glad to get started on
such a function, but I'm also wondering if Nathan would be interested in
giving it a shot? Might also be worthwhile to talk it through on Zoom to
either outline the function or to see if we can find a better approach.
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|
Thanks for getting this started @piersond. Could you hold my hand a little bit, and point me to an example of where the gaps come into play? Also bringing @NateHaywood into this loop. |
@srearl Sorry about the delayed response. I outlined a functional approach to analyte stock calcs by lat-long location last night. I'll touch base when I have the script working and we can all discuss. |
cool and no worries - @NateHaywood is already starting to tune on this so let us keep him in the loop |
The calc_profile_stocks.R script is now functional, though it still needs a lot of proofing, an option to calc stocks using bulk denisty (right now it's doing a profile avg for lyr_soc), and further summary functions to combine near locations. You can see the output for lyr_soc in this table. The 1's and 2's in the table rows are error codes for locations that have only one layer, or have many layers that overlap. @wwieder if you have a few minutes next week, let's discuss the more exact details for the tbl values. i.e. how to combine locations? depth limits? Shouldn't take long to work up those final lyr_soc numbers from where the script stands now. |
How do we do this with the variable experimental structures? missing data? outliers? etc.
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