SRDB import cleanup

[teixeirak]

Here's a running list of things to check/ fix:

• Some plot names repeat "Stand established around [YEAR]"
• Some plot names include "Stand established around NA"
• Plot name "Unmanaged Mature Temperate Evergreen Forest with Clearcut treatment. Stand established around 1980" and any similar ("Clearcut treatment" doesn't make sense) - see issue clarify meaning of "Clearcut" manipulation in relation to stand age #180
• Remove "with No inputs treatment" from plot names
• deal with cases of plots erroneously counted as unmanaged: ForC_private issue #19
• there are a large number of sites labeled "mature" in SRDB but with stand.age<100 (ranging down to 0), and "mature" is not used the same way in SRDB (see SRDB issue 28). Therefore, please change the code such that "Mature" is left out of the name.
• there are four sites labeled "aggrading" in SRDB but with stand.age≥100. Please change the code such that "Aggrading" is left out of the name if stand.age≥100
• there are a handful of plots with treatments ("management" in ForC terminology) that are labeled as "unmanaged". To avoid confusion, let's remove "unmanaged" from these plot names.
• there are a handful of records where ForC.investigator is labeled 'NA' (should be Ben).

[ValentineHerr]

@teixeirak,

About

there are a handful of plots with treatments ("management" in ForC terminology) that are labeled as "unmanaged". To avoid confusion, let's remove "unmanaged" from these plot names.

Below is a table of all combinations of Ecosytem_stage and Manipulation that exist in SRDB (forest and savanna).
I am not sure they all make sense, (example: "Undrained, unplanted" is considered as managed). Also I am not sure "Natural' is always appropriate.
But for unmanaged, does that mean I should keep it only for plots that have "None" or "No inputs" in Ecosytem_stage ?

Also, so far in the code we had "put the manipulation and manipulation level in the plot.name if manipulation is not "None". But I guess it should be "... if manipulation is not "None" nor "No inputs", right ?
Never mind, this is YES.

	Burned	Burned, cleared	Burned, thinned	Burned, understory thinned	Burning	Burning, thinning	Burnt	C. alata addition	CaCl2 added	CaHPO4 added	Clear-cut	Clear-cut, Humus and mineral soil mixed thoroughly to a depth of 30 cm	Clearcut	Clearcut no slash	Clearcut with slash	Clearcut, burning	Clearcut, logging residue	Clearcut, no residue	Clearcut, slash burnt	Clearcut, soil mixing	CO2	CO2, fertilized	CO2, heated	CO2, irrigated	CO2, O3	Deep soil frost	Disk harrowing	Double precipitation	Drained	Drained, planted	Drought	Drought, irrigation	Fertilization	Fertilized	Fertilized, CO2	Fertilized, drained	Fertilized, irrigated	Fertilized, irrigation	Fertilized, thinned	Grazed	Harvest	Heated	Heated (air, soil)	Heated (soil)	Heated, CO2	Heating	Heating, CO2	Herbicide	Herbicide, fertilization	High soil N	High soil N, CO2	Insecticide	Irrigated	Irrigated+fertilized	Irrigation	Irrigation, CO2	Irrigation, CO2, high N	Irrigation, fertilized	Irrigation, high N	Logged	Low soil N	Low soil N, CO2	NaNO3 added	Nitrogen	Nitrogen, CO2	Nitrogen, phosphorous	No inputs	None	O-horizon removed	O3	Organic residues removed	Partial cut	Partial harvest	Post-flush burn	Post-flush cut	Pre-flush burn	Pre-flush cut	Rainfall exclusion	Salvage logging	Scarified	Selection cutting	Shallow soil frost	Soil compaction	Soil warming	Species added	Species added; insecticide	Stem wood harvest	Thinned	Thinned, burned	Thinned, irrigation, fertilized	Thinning	Thinning, Stumps extrated from soil	Throughfall exclusion	Tilled	Tilled, Grazed	Trenching	Understory harvesting	Understory removal	Understory removal, C. alata addition	Understory removed	Understory thinned	Undrained, planted	Undrained, unplanted	Vegetation control	Warmed	Warming	Warming, drought	Weed control	Weed control, irrigation	Weed control, irrigation, fertilized	Weed control, irrigation, fertilized, pest control	Weeding, fertilization	Woody adelgid infestation
Managed	1	0	0	0	3	0	0	1	0	0	2	2	19	2	2	0	3	4	2	1	44	6	4	1	0	0	1	0	16	2	6	2	7	140	2	7	4	0	2	1	21	4	2	2	0	0	0	2	1	2	2	1	2	1	18	4	2	15	2	0	2	2	0	2	2	0	0	750	4	0	4	1	1	0	0	0	0	0	2	0	1	0	0	1	0	1	4	33	0	1	5	2	0	1	1	0	1	3	1	0	0	2	2	8	6	1	0	1	1	1	1	2	0
Natural	7	0	3	3	1	5	1	0	3	3	0	0	13	0	0	2	0	0	0	0	8	0	4	0	0	1	0	1	0	0	22	0	1	59	0	0	0	0	0	0	0	16	0	0	1	2	2	0	0	0	0	0	0	0	15	0	0	0	0	0	0	0	3	1	0	1	4	1883	0	0	0	0	0	3	3	3	3	1	0	1	0	1	1	1	0	0	0	8	1	0	0	0	2	0	0	3	0	0	0	1	3	0	0	0	6	2	3	0	0	0	0	0	2
Unmanaged	2	1	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	2	0	25	0	0	0	9	0	0	2	1	0	2	0	8	8	1	0	0	1	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	1	0	0	0	0	0	0	5	436	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0

[ValentineHerr]

note about

there are a large number of sites labeled "mature" in SRDB but with stand.age<100 (ranging down to 0), and "mature" is not used the same way in SRDB (see SRDB issue 28). Therefore, please change the code such that "Mature" is left out of the name.

Stand.age is coming from Age_disturbance and if that is missing we take Age_ecosystem. Maybe Age_disturbance is not relevant when it is a minor disturbance? That might be why there are so many young plots that are labeled as mature ?

[bpbond]

Hmm, could be. In SRDB Age_disturbance should generally reset with any kind of disturbance.

I am not sure they all make sense, (example: "Undrained, unplanted" is considered as managed). Also I am not sure "Natural' is always appropriate.

There's some fuzziness around the edges, but in general the Natural-Unmanaged-Managed binning is useful I think: "no human influence", "no recent/active human management", "actively managed".

[teixeirak]

I am not sure they all make sense, (example: "Undrained, unplanted" is considered as managed). Also I am not sure "Natural' is always appropriate.

There's some fuzziness around the edges, but in general the Natural-Unmanaged-Managed binning is useful I think: "no human influence", "no recent/active human management", "actively managed".

I think that in many cases, treatments that we count as management may have been applied to natural/ unmanaged stands. That is, the designations in SRDB apply prior to application of experimental treatments. Is this correct, @bpbond ?

[bpbond]

the designations in SRDB apply prior to application of experimental treatments

Right!

[teixeirak]

the designations in SRDB apply prior to application of experimental treatments

@ValentineHerr, this means that we should drop the managed/unmanaged/natural for all stands with treatments and the mature/aggrading designation when the disturbance is stand-clearing.

[ValentineHerr]

@teixeirak,

I I am not sure I understand this....

Here is the current plot.name definition (coming from this issue)
"[Ecosystem_state] [stage] [Biome] [Leaf_habit (changing "mix" to "mixed"] [Ecosystem_type] , with [Manipulation, if any] ([level, if any]) treatment, "stand established around [year of measurement - stand.age] ([if any])"

(note: [stage] is Aggrading, Mature, Natural or NA)

@ValentineHerr, this means that we should drop the managed/unmanaged/natural for all stands with treatments and the mature/aggrading designation when the disturbance is stand-clearing

I think I translate this to:

• If a record
  • has "None" or "No inputs" in Manipulation,
    OR
  • has any Manipulation corresponding to "stand-clearing" in the manipulations.csv AND is "natural" in stage

---> then keep [stage] from the plot.name definition.

• If a record
  • has anything but "None" or "No inputs" in Manipulation, or "stand-clearing"

--> then drop [stage] from the plot.name definition.

Is that correct??

[teixeirak]

Not quite. There are two separate changes.

1:

If a record
    has anything but "None" or "No inputs" in Manipulation, or "stand-clearing"

--> then drop [Ecosystem_state] from the plot.name definition.

[teixeirak]

2: If a record (has any Manipulation corresponding to "stand-clearing" in the manipulations.csv and [stage = mature] )OR if (age<100 years and [stage = mature] ),

---> then drop [stage] from the plot.name definition.

[ValentineHerr]

Is this still valid ?

"there are four sites labeled "aggrading" in SRDB but with stand.age≥100. Please change the code such that "Aggrading" is left out of the name if stand.age≥100"

[teixeirak]

These records have been fixed in SRDB.

[ValentineHerr]

@teixeirak , about

there are a handful of records where ForC.investigator is labeled 'NA' (should be Ben).

see this issue

[ValentineHerr]

there are a handful of plots with treatments ("management" in ForC terminology) that are labeled as "unmanaged". To avoid confusion, let's remove "unmanaged" from these plot names.

I believe this is fixed but @teixeirak can double check (might need to double check in ForC_simplified once I push everything)

[teixeirak]

I actually see a few cases of plots with treatments where "unmanaged" or "natural" remains in the plot name. For example:

• measurement.ID=22056: Unmanaged Aggrading Temperate Deciduous Forest with CO2 (534 ppm) treatment. Stand established around 1997
• measurement.ID=22216: Natural Aggrading Tropical NA Forest with Fertilized treatment. Stand established around 1993.5

I don't think these are hugely problematic or confusing, so if its a pain to fix we can leave it.

[ValentineHerr]

for the first example (SRDB record 1634), it is because it says "unmanaged" in SRDB Ecosystem_state
for the second example (SRDB record 1986) it is because it says "natural" in SRDB Ecosystem_state

I added some code to say
"... OR if Ecosystem_state is "Unmanaged" or "Natural" and manipulation is not c("None", "No inputs"), ... then do not put Ecosystem_state in the plot.name".

Hopefully that will fix the cases you found

[teixeirak]

there are a large number of sites labeled "mature" in SRDB but with stand.age<100 (ranging down to 0), and "mature" is not used the same way in SRDB (see SRDB issue 28). Therefore, please change the code such that "Mature" is left out of the name.

@ValentineHerr, this doesn't seem to have been completely implemented. For example, citation.ID 28417 has plot name "Mature Subtropical Deciduous Forest. Stand established around 1993" and stand.age=19.

[ValentineHerr]

Thanks for catching that Krista, I had not implemented that correctly. It is now fixed in the "with SRDB" branch.

[ValentineHerr]

@teixeirak, the only cases where there is "Mature" in plot.name now is where age is >=100 or "NAC". Is that ok?

[teixeirak]

Yes.

[teixeirak]

You can go ahead and merge into the master now.