Define undefined status
maurolepore opened this issue · 6 comments
maurolepore commented
library(tidyverse)
library(fgeo.data)
tables <- c("bci_stem6_random", "bci_tree6_random", "bci_vft_random")
tables %>%
map(get) %>%
set_names(tables) %>%
map(select, matches("status")) %>%
map(unique) %>%
map(pull) %>%
map(paste, collapse = ", ")
#> $bci_stem6_random
#> [1] "A, V, D, P, G, AR"
#>
#> $bci_tree6_random
#> [1] "A, D, P"
#>
#> $bci_vft_random
#> [1] "alive, broken below, dead, missing"Created on 2018-04-16 by the reprex package (v0.2.0).
maurolepore commented
Hi Suzanne (@laosuz),
Here are the values of status of a stem table from BCI. Could you please direct me to the documentation of their meaning?
(I couldn't find them at http://ctfs.si.edu/Public/CTFSRPackage/index.php/web/data_format/tree_data).
#> $bci_stem6_random
#> [1] "A, V, D, P, G, AR"My interpretation is this:
Alive, I don't know, dead, prior, gone, I don't know.
laosuz commented
Hi Mauro,
Rick wrote the following to explain why he added a V status:
Okay, I fixed this problem. There should be a status 'V' applied to stemIDs present in one census for which there is no record in the next census. This is what happens at BCI for censuses up to 7. The status 'G' is only applied when a stemID has a code indicating the stem is broken or dead.
A tree having at least one stem with 'G' is still alive ('A'). But a tree having all stems with 'V' is missing ('M').
This is fixed in my current code and BCI R tables.
To explain a little:
At BCI, in the first censuses, we did not put tags on the stems of a multiple-stemmed tree. So there was no precise way of linking a stem from a recensus back to the previous censuses. Because of this, we always gave the stems a new StemID in every subsequent census. So Rick decided to give these StemIDs a status of V.
Rick created an algorithm in his BCI R tables to try to link stems in the censuses, where he compared DBHs from one census to the next. That is why our previous BCI R tables are not the same as those that Rick has.
As to the AR code, I’m not sure what it means, maybe alive but diameter is below 1 cm? This refers to stems that were above >=10 mm diameter but in a later census broke and diameter is below 1 cm, but tree is alive.
Hope this helps.
Suzanne
From: Mauro Lepore <notifications@github.com>
Sent: Monday, April 16, 2018 12:52 PM
To: forestgeo/fgeo.data <fgeo.data@noreply.github.com>
Cc: Lao, Suzanne <LAOZ@si.edu>; Mention <mention@noreply.github.com>
Subject: Re: [forestgeo/fgeo.data] Define undefined status (#17)
Hi Suzanne (@laosuz<https://github.com/laosuz>),
Here are the values of status of a stem table from BCI. Could you please direct me to the documentation of their meaning?
(I couldn't find them at http://ctfs.si.edu/Public/CTFSRPackage/index.php/web/data_format/tree_data).
#> $bci_stem6_random
#> [1] "A, V, D, P, G, AR"
My interpretation is this:
Alive, I don't know, dead, prior, gone, I don't know.
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maurolepore commented
Thanks very much Suzanne for explaining.
BCI seems to be different to other datasets in so many ways that I believe
it's not the best dataset for examples. I don't want people to spend energy
thinking how their dataset is different to the example dataset. I want them
so spend energy in understanding whatever function the dataset is being
used to illustrate.
Instead of BCI, can we use Luquillo? I touch on this with Stuart last
Friday and he seemed to be opened to this alternative.
Cheers,
Mauro
…On Mon, Apr 16, 2018 at 3:01 PM, Suzanne Lao ***@***.***> wrote:
Hi Mauro,
Rick wrote the following to explain why he added a V status:
Okay, I fixed this problem. There should be a status 'V' applied to
stemIDs present in one census for which there is no record in the next
census. This is what happens at BCI for censuses up to 7. The status 'G' is
only applied when a stemID has a code indicating the stem is broken or
dead.
A tree having at least one stem with 'G' is still alive ('A'). But a tree
having all stems with 'V' is missing ('M').
This is fixed in my current code and BCI R tables.
To explain a little:
At BCI, in the first censuses, we did not put tags on the stems of a
multiple-stemmed tree. So there was no precise way of linking a stem from a
recensus back to the previous censuses. Because of this, we always gave the
stems a new StemID in every subsequent census. So Rick decided to give
these StemIDs a status of V.
Rick created an algorithm in his BCI R tables to try to link stems in the
censuses, where he compared DBHs from one census to the next. That is why
our previous BCI R tables are not the same as those that Rick has.
As to the AR code, I’m not sure what it means, maybe alive but diameter is
below 1 cm? This refers to stems that were above >=10 mm diameter but in a
later census broke and diameter is below 1 cm, but tree is alive.
Hope this helps.
Suzanne
From: Mauro Lepore ***@***.***>
Sent: Monday, April 16, 2018 12:52 PM
To: forestgeo/fgeo.data ***@***.***>
Cc: Lao, Suzanne ***@***.***>; Mention ***@***.***>
Subject: Re: [forestgeo/fgeo.data] Define undefined status (#17)
Hi Suzanne ***@***.***<https://github.com/laosuz>),
Here are the values of status of a stem table from BCI. Could you please
direct me to the documentation of their meaning?
(I couldn't find them at http://ctfs.si.edu/Public/
CTFSRPackage/index.php/web/data_format/tree_data).
#> $bci_stem6_random
#> [1] "A, V, D, P, G, AR"
My interpretation is this:
Alive, I don't know, dead, prior, gone, I don't know.
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laosuz commented
Hi Mauro,
Yes, the Luquillo dataset is definitely “cleaner”. The only thing is that the mortality rate is extremely high. Maybe you can use the earlier censuses for your examples.
Please make sure that Stuart, as well as Luquillo’s PI (Jess Zimmerman) know that you will be using a subset of Luquillo for your examples.
Best,
Suzanne
From: Mauro Lepore <notifications@github.com>
Sent: Monday, April 16, 2018 2:49 PM
To: forestgeo/fgeo.data <fgeo.data@noreply.github.com>
Cc: Lao, Suzanne <LAOZ@si.edu>; Mention <mention@noreply.github.com>
Subject: Re: [forestgeo/fgeo.data] Define undefined status (#17)
Thanks very much Suzanne for explaining.
BCI seems to be different to other datasets in so many ways that I believe
it's not the best dataset for examples. I don't want people to spend energy
thinking how their dataset is different to the example dataset. I want them
so spend energy in understanding whatever function the dataset is being
used to illustrate.
Instead of BCI, can we use Luquillo? I touch on this with Stuart last
Friday and he seemed to be opened to this alternative.
Cheers,
Mauro
On Mon, Apr 16, 2018 at 3:01 PM, Suzanne Lao ***@***.***> wrote:
Hi Mauro,
Rick wrote the following to explain why he added a V status:
Okay, I fixed this problem. There should be a status 'V' applied to
stemIDs present in one census for which there is no record in the next
census. This is what happens at BCI for censuses up to 7. The status 'G' is
only applied when a stemID has a code indicating the stem is broken or
dead.
A tree having at least one stem with 'G' is still alive ('A'). But a tree
having all stems with 'V' is missing ('M').
This is fixed in my current code and BCI R tables.
To explain a little:
At BCI, in the first censuses, we did not put tags on the stems of a
multiple-stemmed tree. So there was no precise way of linking a stem from a
recensus back to the previous censuses. Because of this, we always gave the
stems a new StemID in every subsequent census. So Rick decided to give
these StemIDs a status of V.
Rick created an algorithm in his BCI R tables to try to link stems in the
censuses, where he compared DBHs from one census to the next. That is why
our previous BCI R tables are not the same as those that Rick has.
As to the AR code, I’m not sure what it means, maybe alive but diameter is
below 1 cm? This refers to stems that were above >=10 mm diameter but in a
later census broke and diameter is below 1 cm, but tree is alive.
Hope this helps.
Suzanne
From: Mauro Lepore ***@***.***>
Sent: Monday, April 16, 2018 12:52 PM
To: forestgeo/fgeo.data ***@***.***>
Cc: Lao, Suzanne ***@***.***>; Mention ***@***.***>
Subject: Re: [forestgeo/fgeo.data] Define undefined status (#17)
Hi Suzanne ***@***.***<https://github.com/laosuz>),
Here are the values of status of a stem table from BCI. Could you please
direct me to the documentation of their meaning?
(I couldn't find them at http://ctfs.si.edu/Public/
CTFSRPackage/index.php/web/data_format/tree_data).
#> $bci_stem6_random
#> [1] "A, V, D, P, G, AR"
My interpretation is this:
Alive, I don't know, dead, prior, gone, I don't know.
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maurolepore commented
test
maurolepore commented
Closing. Instead, using data from Luquillo.